Clinical Focus

  • Emergency Medicine
  • Infectious Diseases
  • Immunology
  • Biomedical Engineering
  • Systems Biology
  • Machine Learning

Academic Appointments

Boards, Advisory Committees, Professional Organizations

  • Grant Reviewer, NIH, DoD-CDMRP, MRC-UK, Wellcome Trust (2011 - Present)

Professional Education

  • Board Certification: American Board of Emergency Medicine, Emergency Medicine (2007)
  • Fellowship: Johns Hopkins University School of Medicine (2004) MD
  • Residency: Johns Hopkins University School of Medicine (2002) MD
  • Medical Education: University of California, Los Angeles (1999) CA
  • Undergraduate, Massachusetts Institute of Technology, B.S. (1994)

Current Research and Scholarly Interests

Dr. Yang's research is focused on bridging the translational gap at the interface of molecular biology, genome science, engineering, and acute care medicine. The investigative interest of the Yang lab falls within the general theme of developing integrative systems-level approaches for precision diagnostics, as well as data driven knowledge discoveries, to improve the health outcome and our understanding of complex critical illnesses. Using sepsis and COVID-19 as the disease models with complex host-pathogen dynamics, the goals of the Yang lab are divided into 2 areas:

1) Developing high-content, near-patient, diagnostic system for rapid broad pathogen detection and characterization.

2) Integrating multi-omics molecular and phenotypic data layers with novel computational approaches into advanced diagnostics and predictive analytics for acute infections.

Clinical Trials

  • SEP-SEQ Trial - Determining the Etiology of Sepsis Using an Infectious Disease Diagnostic Sequencing Assay Not Recruiting

    The purpose of this study is to evaluate the performance of the Karius Infectious Diseases Plasma Sequencing Assay in patients who present to the emergency room with sepsis.

    Stanford is currently not accepting patients for this trial.

    View full details

2023-24 Courses

Stanford Advisees

All Publications

  • Re-visiting humoral constitutive antibacterial heterogeneity in bloodstream infections. The Lancet. Infectious diseases Abe, R., Ram-Mohan, N., Yang, S. 2023


    Although cellular immunity has garnered much attention in the era of single-cell technologies, humoral innate immunity has receded in priority due to its presumed limited roles. Hence, despite the long-recognised bactericidal activity of serum-a functional characteristic of constitutive humoral immunity-much remains unclear regarding mechanisms underlying its inter-individual heterogeneity and clinical implications in bloodstream infections. Recent work suggests that the immediate antimicrobial effect of humoral innate immunity contributes to suppression of the excessive inflammatory responses to infection by reducing the amount of pathogen-associated molecular patterns. In this Personal View, we propose the need to re-explore factors underlying the inter-individual heterogeneity in serum antibacterial competence as a new approach to better understand humoral innate immunity and revisit the clinical use of measuring serum antibacterial activity in the management of bacterial bloodstream infections. Given the current emphasis on subtyping sepsis, a serum bactericidal assay might prove useful in defining a distinct sepsis endotype, to enable more personalised management.

    View details for DOI 10.1016/S1473-3099(23)00494-2

    View details for PubMedID 37944543

  • SARS-CoV-2 RNAemia predicts clinical deterioration and extrapulmonary complications from COVID-19. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Ram-Mohan, N. n., Kim, D. n., Zudock, E. J., Hashemi, M. M., Tjandra, K. C., Rogers, A. J., Blish, C. A., Nadeau, K. C., Newberry, J. A., Quinn, J. V., O'Hara, R. n., Ashley, E. n., Nguyen, H. n., Jiang, L. n., Hung, P. n., Blomkalns, A. L., Yang, S. n. 2021


    The determinants of COVID-19 disease severity and extrapulmonary complications (EPCs) are poorly understood. We characterized relationships between SARS-CoV-2 RNAemia and disease severity, clinical deterioration, and specific EPCs.We used quantitative (qPCR) and digital (dPCR) PCR to quantify SARS-CoV-2 RNA from plasma in 191 patients presenting to the Emergency Department (ED) with COVID-19. We recorded patient symptoms, laboratory markers, and clinical outcomes, with a focus on oxygen requirements over time. We collected longitudinal plasma samples from a subset of patients. We characterized the role of RNAemia in predicting clinical severity and EPCs using elastic net regression.23.0% (44/191) of SARS-CoV-2 positive patients had viral RNA detected in plasma by dPCR, compared to 1.4% (2/147) by qPCR. Most patients with serial measurements had undetectable RNAemia within 10 days of symptom onset, reached maximum clinical severity within 16 days, and symptom resolution within 33 days. Initially RNAaemic patients were more likely to manifest severe disease (OR 6.72 [95% CI, 2.45 - 19.79]), worsening of disease severity (OR 2.43 [95% CI, 1.07 - 5.38]), and EPCs (OR 2.81 [95% CI, 1.26 - 6.36]). RNA load correlated with maximum severity (r = 0.47 [95% CI, 0.20 - 0.67]).dPCR is more sensitive than qPCR for the detection of SARS-CoV-2 RNAemia, which is a robust predictor of eventual COVID-19 severity and oxygen requirements, as well as EPCs. Since many COVID-19 therapies are initiated on the basis of oxygen requirements, RNAemia on presentation might serve to direct early initiation of appropriate therapies for the patients most likely to deteriorate.

    View details for DOI 10.1093/cid/ciab394

    View details for PubMedID 33949665

  • Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection. Life science alliance Ram-Mohan, N., Thair, S. A., Litzenburger, U. M., Cogill, S., Andini, N., Yang, X., Chang, H. Y., Yang, S. 2021; 4 (8)


    Sepsis, sequela of bloodstream infections and dysregulated host responses, is a leading cause of death globally. Neutrophils tightly regulate responses to pathogens to prevent organ damage. Profiling early host epigenetic responses in neutrophils may aid in disease recognition. We performed assay for transposase-accessible chromatin (ATAC)-seq of human neutrophils challenged with six toll-like receptor ligands and two organisms; and RNA-seq after Escherichia coli exposure for 1 and 4 h along with ATAC-seq. ATAC-seq of neutrophils facilitates detection of pathogen DNA. In addition, despite similarities in genomic distribution of differential chromatin changes across challenges, only a fraction overlaps between the challenges. Ligands depict shared signatures, but majority are unique in position, function, and challenge. Epigenomic changes are plastic, only ∼120 are shared by Ecoli challenges over time, resulting in varied differential genes and associated processes. We identify three classes of gene regulation, chromatin access changes in the promoter; changes in the promoter and distal enhancers; and controlling expression through changes solely in distal enhancers. These and transcription factor footprinting reveal timely and challenge specific mechanisms of transcriptional regulation in neutrophils.

    View details for DOI 10.26508/lsa.202000976

    View details for PubMedID 34145026

  • Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nature microbiology Blauwkamp, T. A., Thair, S., Rosen, M. J., Blair, L., Lindner, M. S., Vilfan, I. D., Kawli, T., Christians, F. C., Venkatasubrahmanyam, S., Wall, G. D., Cheung, A., Rogers, Z. N., Meshulam-Simon, G., Huijse, L., Balakrishnan, S., Quinn, J. V., Hollemon, D., Hong, D. K., Vaughn, M. L., Kertesz, M., Bercovici, S., Wilber, J. C., Yang, S. 2019


    Thousands of pathogens are known to infect humans, but only a fraction are readily identifiable using current diagnostic methods. Microbial cell-free DNA sequencing offers the potential to non-invasively identify a wide range of infections throughout the body, but the challenges of clinical-grade metagenomic testing must be addressed. Here we describe the analytical and clinical validation of a next-generation sequencing test that identifies and quantifies microbial cell-free DNA in plasma from 1,250 clinically relevant bacteria, DNA viruses, fungi and eukaryotic parasites. Test accuracy, precision, bias and robustness to a number of metagenomics-specific challenges were determined using a panel of 13 microorganisms that model key determinants of performance in 358 contrived plasma samples, as well as 2,625 infections simulated in silico and 580 clinical study samples. The test showed 93.7% agreement with blood culture in a cohort of 350 patients with a sepsis alert and identified an independently adjudicated cause of the sepsis alert more often than all of the microbiological testing combined (169 aetiological determinations versus 132). Among the 166 samples adjudicated to have no sepsis aetiology identified by any of the tested methods, sequencing identified microbial cell-free DNA in 62, likely derived from commensal organisms and incidental findings unrelated to the sepsis alert. Analysis of the first 2,000 patient samples tested in the CLIA laboratory showed that more than 85% of results were delivered the day after sample receipt, with 53.7% of reports identifying one or more microorganisms.

    View details for PubMedID 30742071

  • A "Culture" Shift: Broad Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing Directly from Whole Blood. Clinical chemistry Andini, N., Hu, A., Zhou, L., Cogill, S., Wang, T., Wittwer, C. T., Yang, S. 2018


    BACKGROUND: The time required for bloodstream pathogen detection, identification (ID), and antimicrobial susceptibility testing (AST) does not satisfy the acute needs of disease management. Conventional methods take up to 3 days for ID and AST. Molecular diagnostics have reduced times for ID, but their promise to supplant culture is unmet because AST times remain slow. We developed a combined quantitative PCR (qPCR)-based ID+AST assay with sequential detection, ID, and AST of leading nosocomial bacterial pathogens.METHODS: ID+AST was performed on whole blood samples by (a) removing blood cells, (b) brief bacterial enrichment, (c) bacterial detection and ID, and (d) species-specific antimicrobial treatment. Broad-spectrum qPCR of the internal transcribed spacer between the 16S and 23S was amplified for detection. High-resolution melting identified the species with a curve classifier. AST was enabled by Ct differences between treated and untreated samples.RESULTS: A detection limit of 1 CFU/mL was achieved for Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. All species were accurately identified by unique melting curves. Antimicrobial minimum inhibitory concentrations were identified with Ct differences of ≥1 cycle. Using an RNA target allowed reduction of AST incubation time from 60 min to 5 min. Rapid-cycle amplification reduced qPCR times by 83% to 30 min.CONCLUSIONS: Combined, sequential ID+AST protocols allow rapid and reliable detection, ID, and AST for the diagnosis of bloodstream infections, enabling conversion of empiric to targeted therapy by the second dose of antimicrobials.

    View details for PubMedID 30087140

  • Universal digital high-resolution melt: a novel approach to broad-based profiling of heterogeneous biological samples NUCLEIC ACIDS RESEARCH Fraley, S. I., Hardick, J., Masek, B. J., Athamanolap, P., Rothman, R. E., Gaydos, C. A., Carroll, K. C., Wakefield, T., Wang, T., Yang, S. 2013; 41 (18)


    Comprehensive profiling of nucleic acids in genetically heterogeneous samples is important for clinical and basic research applications. Universal digital high-resolution melt (U-dHRM) is a new approach to broad-based PCR diagnostics and profiling technologies that can overcome issues of poor sensitivity due to contaminating nucleic acids and poor specificity due to primer or probe hybridization inaccuracies for single nucleotide variations. The U-dHRM approach uses broad-based primers or ligated adapter sequences to universally amplify all nucleic acid molecules in a heterogeneous sample, which have been partitioned, as in digital PCR. Extensive assay optimization enables direct sequence identification by algorithm-based matching of melt curve shape and Tm to a database of known sequence-specific melt curves. We show that single-molecule detection and single nucleotide sensitivity is possible. The feasibility and utility of U-dHRM is demonstrated through detection of bacteria associated with polymicrobial blood infection and microRNAs (miRNAs) associated with host response to infection. U-dHRM using broad-based 16S rRNA gene primers demonstrates universal single cell detection of bacterial pathogens, even in the presence of larger amounts of contaminating bacteria; U-dHRM using universally adapted Lethal-7 miRNAs in a heterogeneous mixture showcases the single copy sensitivity and single nucleotide specificity of this approach.

    View details for DOI 10.1093/nar/gkt684

    View details for Web of Science ID 000325776600006

    View details for PubMedID 23935121

    View details for PubMedCentralID PMC3794612

  • Molecular methods for pathogen detection in blood LANCET Lin, S., Yang, S. 2010; 375 (9710): 178-179
  • PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings LANCET INFECTIOUS DISEASES Yang, S., Rothman, R. E. 2004; 4 (6): 337-348


    Molecular diagnostics are revolutionising the clinical practice of infectious disease. Their effects will be significant in acute-care settings where timely and accurate diagnostic tools are critical for patient treatment decisions and outcomes. PCR is the most well-developed molecular technique up to now, and has a wide range of already fulfilled, and potential, clinical applications, including specific or broad-spectrum pathogen detection, evaluation of emerging novel infections, surveillance, early detection of biothreat agents, and antimicrobial resistance profiling. PCR-based methods may also be cost effective relative to traditional testing procedures. Further advancement of technology is needed to improve automation, optimise detection sensitivity and specificity, and expand the capacity to detect multiple targets simultaneously (multiplexing). This review provides an up-to-date look at the general principles, diagnostic value, and limitations of the most current PCR-based platforms as they evolve from bench to bedside.

    View details for Web of Science ID 000221799100020

    View details for PubMedID 15172342

  • IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. Nature communications Haslund-Gourley, B. S., Woloszczuk, K., Hou, J., Connors, J., Cusimano, G., Bell, M., Taramangalam, B., Fourati, S., Mege, N., Bernui, M., Altman, M. C., Krammer, F., van Bakel, H., IMPACC Network, Maecker, H. T., Rouphael, N., Diray-Arce, J., Wigdahl, B., Kutzler, M. A., Cairns, C. B., Haddad, E. K., Comunale, M. A., Ozonoff, A., Ehrlich, L. I., Melamed, E., Sesma, A. F., Simon, V., Pulendran, B., Nadeau, K. C., Davis, M. M., McCoey, G. A., Sekaly, R., Baden, L. R., Levy, O., Schaenman, J., Reed, E. F., Shaw, A. C., Hafler, D. A., Montgomery, R. R., Kleinstein, S. H., Becker, P. M., Augustine, A. D., Calfee, C. S., Erle, D. J., DeBakey, M. E., Corry, D. B., Kheradmand, F., Atkinson, M. A., Brakenridge, S. C., Higuita, N. I., Metcalf, J. P., Hough, C. L., Messer, W. B., Kraft, M., Bime, C., Peters, B., Milliren, C. E., Syphurs, C., McEnaney, K., Barton, B., Lentucci, C., Saluvan, M., Chang, A. C., Hoch, A., Albert, M., Shaheen, T., Kho, A. T., Liu, S., Thomas, S., Chen, J., Murphy, M. D., Cooney, M., Hayati, A. N., Bryant, R., Abraham, J., Jayavelu, N. D., Presnell, S., Jancsyk, T., Maguire, C., Qi, J., Lee, B., Fourati, S., Esserman, D. A., Guan, L., Gygi, J., Pawar, S., Brito, A., Fragiadakis, G. K., Patel, R., Overton, J. A., Vita, R., Westendorf, K., Shannon, C. P., Tebbutt, S. J., Thyagarajan, R. V., Rousseau, J. F., Wylie, D., Triplett, T. A., Kojic, E., Chinthrajah, S., Ahuja, N., Rogers, A. J., Artandi, M., Geng, L., Yendewa, G., Powell, D. L., Kim, J. N., Simmons, B., Goonewardene, I. M., Smith, C. M., Martens, M., Sherman, A. C., Walsh, S. R., Issa, N. C., Salehi-Rad, R., Dela Cruz, C., Farhadian, S., Iwasaki, A., Ko, A. I., Anderson, E. J., Mehta, A. K., Sevransky, J. E., Seyfert-Margolis, V., Leligdowicz, A., Matthay, M. A., Singer, J. P., Kangelaris, K. N., Hendrickson, C. M., Krummel, M. F., Langelier, C. R., Woodruff, P. G., Corry, D. B., Kheradmand, F., Anderson, M. L., Guirgis, F. W., Drevets, D. A., Brown, B. R., Siegel, S. A., Lu, Z., Mosier, J., Kimura, H., Khor, B., van Bakel, H., Rahman, A., Stadlbauer, D., Dutta, J., Xie, H., Kim-Schulze, S., Gonzalez-Reiche, A. S., van de Guchte, A., Carreno, J. M., Singh, G., Raskin, A., Tcheou, J., Bielak, D., Kawabata, H., Kelly, G., Patel, M., Nie, K., Yellin, T., Fried, M., Sullivan, L., Morris, S., Sieg, S., Steen, H., van Zalm, P., Fatou, B., Mendez, K., Lasky-Su, J., Hutton, S. R., Michelotti, G., Wong, K., Jha, M., Viode, A., Kanarek, N., Petrova, B., Zhao, Y., Bosinger, S. E., Boddapati, A. K., Tharp, G. K., Pellegrini, K. L., Beagle, E., Cowan, D., Hamilton, S., Ribeiro, S. P., Hodder, T., Rosen, L. B., Lee, S., Wilson, M. R., Dandekar, R., Alvarenga, B., Rajan, J., Eckalbar, W., Schroeder, A. W., Tsitsiklis, A., Mick, E., Guerrero, Y. S., Love, C., Maliskova, L., Adkisson, M., Siles, N., Geltman, J., Hurley, K., Saksena, M., Altman, D., Srivastava, K., Eaker, L. Q., Bermudez-Gonzalez, M. C., Beach, K. F., Sominsky, L. A., Azad, A. R., Mulder, L. C., Kleiner, G., Lee, A. S., Do, E., Fernandes, A., Manohar, M., Hagan, T., Blish, C. A., Din, H. N., Roque, J., Yang, S., Sigal, N., Chang, I., Tribout, H., Harris, P., Consolo, M., Edwards, C., Lee, E., Lin, E., Croen, B., Semenza, N. C., Rogowski, B., Melnyk, N., Bell, M. R., Furukawa, S., McLin, R., Schearer, P., Sheidy, J., Tegos, G. P., Nagle, C., Smolen, K., Desjardins, M., van Haren, S., Mitre, X., Cauley, J., Li, X., Tong, A., Evans, B., Montesano, C., Licona, J. H., Krauss, J., Chang, J. B., Izaguirre, N., Rooks, R., Elashoff, D., Brook, J., Ramires-Sanchez, E., Llamas, M., Rivera, A., Perdomo, C., Ward, D. C., Magyar, C. E., Fulcher, J. A., Pickering, H. C., Sen, S., Chaudhary, O., Coppi, A., Fournier, J., Mohanty, S., Muenker, C., Nelson, A., Raddassi, K., Rainone, M., Ruff, W. E., Salahuddin, S., Schulz, W. L., Vijayakumar, P., Wang, H., Wunder, E. J., Young, H. P., Rothman, J., Konstorum, A., Chen, E., Cotsapas, C., Grubaugh, N. D., Wang, X., Xu, L., Asashima, H., Bristow, L., Hussaini, L., Hellmeister, K., Samaha, H., Wimalasena, S. T., Cheng, A., Spainhour, C., Scherer, E. M., Johnson, B., Bechnak, A., Ciric, C. R., Hewitt, L., Carter, E., Mcnair, N., Panganiban, B., Huerta, C., Usher, J., Vaysman, T., Holland, S. M., Abe-Jones, Y., Asthana, S., Beagle, A., Bhide, S., Carrillo, S. A., Chak, S., Ghale, R., Gonzalez, A., Jauregui, A., Jones, N., Lea, T., Lee, D., Lota, R., Milush, J., Nguyen, V., Pierce, L., Prasad, P. A., Rao, A., Samad, B., Shaw, C., Sigman, A., Sinha, P., Ward, A., Willmore, A., Zhan, J., Rashid, S., Rodriguez, N., Tang, K., Altamirano, L. T., Betancourt, L., Curiel, C., Sutter, N., Paz, M. T., Tietje-Ulrich, G., Leroux, C., Thakur, N., Vasquez, J. J., Santhosh, L., Song, L., Nelson, E., Moldawer, L. L., Borresen, B., Roth-Manning, B., Ungaro, R. F., Oberhaus, J., Booth, J. L., Sinko, L. A., Brunton, A., Sullivan, P. E., Strnad, M., Lyski, Z. L., Coulter, F. J., Micheleti, C., Conway, M., Francisco, D., Molzahn, A., Erickson, H., Wilson, C. C., Schunk, R., Sierra, B., Hughes, T. 2024; 15 (1): 404


    The glycosylation of IgG plays a critical role during human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, activating immune cells and inducing cytokine production. However, the role of IgM N-glycosylation has not been studied during human acute viral infection. The analysis of IgM N-glycosylation from healthy controls and hospitalized coronavirus disease 2019 (COVID-19) patients reveals increased high-mannose and sialylation that correlates with COVID-19 severity. These trends are confirmed within SARS-CoV-2-specific immunoglobulin N-glycan profiles. Moreover, the degree of total IgM mannosylation and sialylation correlate significantly with markers of disease severity. We link the changes of IgM N-glycosylation with the expression of Golgi glycosyltransferases. Lastly, we observe antigen-specific IgM antibody-dependent complement deposition is elevated in severe COVID-19 patients and modulated by exoglycosidase digestion. Taken together, this work links the IgM N-glycosylation with COVID-19 severity and highlights the need to understand IgM glycosylation and downstream immune function during human disease.

    View details for DOI 10.1038/s41467-023-44211-0

    View details for PubMedID 38195739

  • Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. Nature communications Ozonoff, A., Jayavelu, N. D., Liu, S., Melamed, E., Milliren, C. E., Qi, J., Geng, L. N., McComsey, G. A., Cairns, C. B., Baden, L. R., Schaenman, J., Shaw, A. C., Samaha, H., Seyfert-Margolis, V., Krammer, F., Rosen, L. B., Steen, H., Syphurs, C., Dandekar, R., Shannon, C. P., Sekaly, R. P., Ehrlich, L. I., Corry, D. B., Kheradmand, F., Atkinson, M. A., Brakenridge, S. C., Higuita, N. I., Metcalf, J. P., Hough, C. L., Messer, W. B., Pulendran, B., Nadeau, K. C., Davis, M. M., Sesma, A. F., Simon, V., van Bakel, H., Kim-Schulze, S., Hafler, D. A., Levy, O., Kraft, M., Bime, C., Haddad, E. K., Calfee, C. S., Erle, D. J., Langelier, C. R., Eckalbar, W., Bosinger, S. E., Peters, B., Kleinstein, S. H., Reed, E. F., Augustine, A. D., Diray-Arce, J., Maecker, H. T., Altman, M. C., Montgomery, R. R., Becker, P. M., Rouphael, N. 2024; 15 (1): 216


    Post-acute sequelae of SARS-CoV-2 (PASC) is a significant public health concern. We describe Patient Reported Outcomes (PROs) on 590 participants prospectively assessed from hospital admission for COVID-19 through one year after discharge. Modeling identified 4 PRO clusters based on reported deficits (minimal, physical, mental/cognitive, and multidomain), supporting heterogenous clinical presentations in PASC, with sub-phenotypes associated with female sex and distinctive comorbidities. During the acute phase of disease, a higher respiratory SARS-CoV-2 viral burden and lower Receptor Binding Domain and Spike antibody titers were associated with both the physical predominant and the multidomain deficit clusters. A lower frequency of circulating B lymphocytes by mass cytometry (CyTOF) was observed in the multidomain deficit cluster. Circulating fibroblast growth factor 21 (FGF21) was significantly elevated in the mental/cognitive predominant and the multidomain clusters. Future efforts to link PASC to acute anti-viral host responses may help to better target treatment and prevention of PASC.

    View details for DOI 10.1038/s41467-023-44090-5

    View details for PubMedID 38172101

    View details for PubMedCentralID PMC10764789

  • Comparative study of encoded and alignment-based methods for virus taxonomy classification. Scientific reports Shaukat, M. A., Nguyen, T. T., Hsu, E. B., Yang, S., Bhatti, A. 2023; 13 (1): 18662


    The emergence of viruses and their variants has made virus taxonomy more important than ever before in controlling the spread of diseases. The creation of efficient treatments and cures that target particular virus properties can be aided by understanding virus taxonomy. Alignment-based methods are commonly used for this task, but are computationally expensive and time-consuming, especially when dealing with large datasets or when detecting new virus variants is time sensitive. An alternative approach, the encoded method, has been developed that does not require prior sequence alignment and provides faster results. However, each encoded method has its own claimed accuracy. Therefore, careful evaluation and comparison of the performance of different encoded methods are essential to identify the most accurate and reliable approach for virus taxonomy classification. This study aims to address this issue by providing a comprehensive and comparative analysis of the potential of encoded methods for virus classification and phylogenetics. We compared the vectors generated for each encoded method using distance metrics to determine their similarity to alignment-based methods. The results and their validation show that K-merNV followed by CgrDft encoded methods, perform similarly to state-of-the-art multi-sequence alignment methods. This is the first study to incorporate and compare encoded methods that will facilitate future research in making more informed decisions regarding selection of a suitable method for virus taxonomy.

    View details for DOI 10.1038/s41598-023-45461-0

    View details for PubMedID 37907535

    View details for PubMedCentralID 9005552

  • Neutrophil Extracellular Traps have DNAzyme activity that drives bactericidal potential. bioRxiv : the preprint server for biology Ku, T., Ram-Mohan, N., Zudock, E. J., Abe, R., Yang, S. 2023


    The mechanisms of bacterial killing by neutrophil extracellular traps (NETs) are unclear. DNA, the largest component of NETs is believed to merely be a scaffold with minimal antimicrobial activity through the charge of the backbone. Here, we report that NETs DNA is beyond a scaffold and produces hydroxyl free radicals through the spatially concentrated G-quadruplex/hemin DNAzyme complexes, driving bactericidal effects. Immunofluorescence staining showed colocalization of G-quadruplex and hemin in extruded NETs DNA, and Amplex UltraRed assay portrayed its peroxidase activity. Proximity labeling of bacteria revealed localized concentration of radicals resulting from NETs bacterial trapping. Ex vivo bactericidal assays revealed that G-quadruplex/hemin DNAzyme is the primary driver of bactericidal activity in NETs. NETs are DNAzymes that may have important biological consequences.One-Sentence Summary: G-quadruplex/hemin DNAzymes may be major contributors to biological consequences of neutrophil extracellular traps.

    View details for DOI 10.1101/2023.10.23.563618

    View details for PubMedID 37961380

  • Development and external validation of a pretrained deep learning model for the prediction of non-accidental trauma. NPJ digital medicine Huang, D., Cogill, S., Hsia, R. Y., Yang, S., Kim, D. 2023; 6 (1): 131


    Non-accidental trauma (NAT) is deadly and difficult to predict. Transformer models pretrained on large datasets have recently produced state of the art performance on diverse prediction tasks, but the optimal pretraining strategies for diagnostic predictions are not known. Here we report the development and external validation of Pretrained and Adapted BERT for Longitudinal Outcomes (PABLO), a transformer-based deep learning model with multitask clinical pretraining, to identify patients who will receive a diagnosis of NAT in the next year. We develop a clinical interface to visualize patient trajectories, model predictions, and individual risk factors. In two comprehensive statewide databases, approximately 1% of patients experience NAT within one year of prediction. PABLO predicts NAT events with area under the receiver operating characteristic curve (AUROC) of 0.844 (95% CI 0.838-0.851) in the California test set, and 0.849 (95% CI 0.846-0.851) on external validation in Florida, outperforming comparator models. Multitask pretraining significantly improves model performance. Attribution analysis shows substance use, psychiatric, and injury diagnoses, in the context of age and racial demographics, as influential predictors of NAT. As a clinical decision support system, PABLO can identify high-risk patients and patient-specific risk factors, which can be used to target secondary screening and preventive interventions at the point-of-care.

    View details for DOI 10.1038/s41746-023-00875-y

    View details for PubMedID 37468526

    View details for PubMedCentralID PMC10356774

  • Phage diversity in cell-free DNA identifies bacterial pathogens in human sepsis cases. Nature microbiology Haddock, N. L., Barkal, L. J., Ram-Mohan, N., Kaber, G., Chiu, C. Y., Bhatt, A. S., Yang, S., Bollyky, P. L. 2023


    Bacteriophages, viruses that infect bacteria, have great specificity for their bacterial hosts at the strain and species level. However, the relationship between the phageome and associated bacterial population dynamics is unclear. Here we generated a computational pipeline to identify sequences associated with bacteriophages and their bacterial hosts in cell-free DNA from plasma samples. Analysis of two independent cohorts, including a Stanford Cohort of 61 septic patients and 10 controls and the SeqStudy cohort of 224 septic patients and 167 controls, reveals a circulating phageome in the plasma of all sampled individuals. Moreover, infection is associated with overrepresentation of pathogen-specific phages, allowing for identification of bacterial pathogens. We find that information on phage diversity enables identification of the bacteria that produced these phages, including pathovariant strains of Escherichia coli. Phage sequences can likewise be used to distinguish between closely related bacterial species such as Staphylococcus aureus, a frequent pathogen, and coagulase-negative Staphylococcus, a frequent contaminant. Phage cell-free DNA may have utility in studying bacterial infections.

    View details for DOI 10.1038/s41564-023-01406-x

    View details for PubMedID 37308590

    View details for PubMedCentralID 5594678

  • Rapid Molecular Phenotypic Antimicrobial Susceptibility Test for Neisseria gonorrhoeae Based on Propidium Monoazide Viability PCR. ACS infectious diseases Tjandra, K. C., Ram-Mohan, N., Abe, R., Wang, T. H., Yang, S. 2023


    Neisseria gonorrhoeae (NG) is an urgent threat to antimicrobial resistance (AMR) worldwide. NG has acquired rapid resistance to all previously recommended treatments, leaving ceftriaxone monotherapy as the first and last line of therapy for uncomplicated NG. The ability to rapidly determine susceptibility, which is currently nonexistent for NG, has been proposed as a strategy to preserve ceftriaxone by using alternative treatments. Herein, we used a DNA-intercalating dye in combination with NG-specific primers/probes to generate qPCR cycle threshold (Ct) values at different concentrations of 2 NG-relevant antimicrobials. Our proof-of-concept dual-antimicrobial logistic regression model based on the differential Ct measurements achieved an AUC of 0.93 with a categorical agreement for the susceptibility of 84.6%. When surveying the performance against each antimicrobial separately, the model predicted 90 and 75% susceptible and resistant strains, respectively, to ceftriaxone and 66.7 and 83.3% susceptible and resistant strains, respectively, to ciprofloxacin. We further validated the model against the individual replicates and determined the accuracy of the model in classifying susceptibility agnostic of the inoculum size. We demonstrated a novel PCR-based approach to determine phenotypic ciprofloxacin and ceftriaxone susceptibility information for NG with reasonable accuracy within 30 min, a significant improvement compared to the conventional method which could take multiple days.

    View details for DOI 10.1021/acsinfecdis.3c00096

    View details for PubMedID 37115656

  • Development of a Definition of Postacute Sequelae of SARS-CoV-2 Infection. JAMA Thaweethai, T., Jolley, S. E., Karlson, E. W., Levitan, E. B., Levy, B., McComsey, G. A., McCorkell, L., Nadkarni, G. N., Parthasarathy, S., Singh, U., Walker, T. A., Selvaggi, C. A., Shinnick, D. J., Schulte, C. C., Atchley-Challenner, R., Horwitz, L. I., Foulkes, A. S., RECOVER Consortium, Alba, G. A., Alicic, R., Altman, N., Anglin, K., Argueta, U., Ashktorab, H., Baslet, G., Bassett, I. V., Bateman, L., Bedi, B., Bhattacharyya, S., Bind, M., Blomkalns, A. L., Bonilla, H., Bush, P. A., Castro, M., Chan, J., Charney, A. W., Chen, P., Chibnik, L. B., Chu, H. Y., Clifton, R. G., Costantine, M. M., Cribbs, S. K., Davila Nieves, S. I., Deeks, S. G., Duven, A., Emery, I. F., Erdmann, N., Erlandson, K. M., Ernst, K. C., Farah-Abraham, R., Farner, C. E., Feuerriegel, E. M., Fleurimont, J., Fonseca, V., Franko, N., Gainer, V., Gander, J. C., Gardner, E. M., Geng, L. N., Gibson, K. S., Go, M., Goldman, J. D., Grebe, H., Greenway, F. L., Habli, M., Hafner, J., Han, J. E., Hanson, K. A., Heath, J., Hernandez, C., Hess, R., Hodder, S. L., Hoffman, M. K., Hoover, S. E., Huang, B., Hughes, B. L., Jagannathan, P., John, J., Jordan, M. R., Katz, S. D., Kaufman, E. S., Kelly, J. D., Kelly, S. W., Kemp, M. M., Kirwan, J. P., Klein, J. D., Knox, K. S., Krishnan, J. A., Kumar, A., Laiyemo, A. O., Lambert, A. A., Lanca, M., Lee-Iannotti, J. K., Logarbo, B. P., Longo, M. T., Luciano, C. A., Lutrick, K., Maley, J. H., Marathe, J. G., Marconi, V., Marshall, G. D., Martin, C. F., Matusov, Y., Mehari, A., Mendez-Figueroa, H., Mermelstein, R., Metz, T. D., Morse, R., Mosier, J., Mouchati, C., Mullington, J., Murphy, S. N., Neuman, R. B., Nikolich, J. Z., Ofotokun, I., Ojemakinde, E., Palatnik, A., Palomares, K., Parimon, T., Parry, S., Patterson, J. E., Patterson, T. F., Patzer, R. E., Peluso, M. J., Pemu, P., Pettker, C. M., Plunkett, B. A., Pogreba-Brown, K., Poppas, A., Quigley, J. G., Reddy, U., Reece, R., Reeder, H., Reeves, W. B., Reiman, E. M., Rischard, F., Rosand, J., Rouse, D. J., Ruff, A., Saade, G., Sandoval, G. J., Schlater, S. M., Shepherd, F., Sherif, Z. A., Simhan, H., Singer, N. G., Skupski, D. W., Sowles, A., Sparks, J. A., Sukhera, F. I., Taylor, B. S., Teunis, L., Thomas, R. J., Thorp, J. M., Thuluvath, P., Ticotsky, A., Tita, A. T., Tuttle, K. R., Urdaneta, A. E., Valdivieso, D., VanWagoner, T. M., Vasey, A., Verduzco-Gutierrez, M., Wallace, Z. S., Ward, H. D., Warren, D. E., Weiner, S. J., Welch, S., Whiteheart, S. W., Wiley, Z., Wisnivesky, J. P., Yee, L. M., Zisis, S. 2023


    Importance: SARS-CoV-2 infection is associated with persistent, relapsing, or new symptoms or other health effects occurring after acute infection, termed postacute sequelae of SARS-CoV-2 infection (PASC), also known as long COVID. Characterizing PASC requires analysis of prospectively and uniformly collected data from diverse uninfected and infected individuals.Objective: To develop a definition of PASC using self-reported symptoms and describe PASC frequencies across cohorts, vaccination status, and number of infections.Design, Setting, and Participants: Prospective observational cohort study of adults with and without SARS-CoV-2 infection at 85 enrolling sites (hospitals, health centers, community organizations) located in 33 states plus Washington, DC, and Puerto Rico. Participants who were enrolled in the RECOVER adult cohort before April 10, 2023, completed a symptom survey 6 months or more after acute symptom onset or test date. Selection included population-based, volunteer, and convenience sampling.Exposure: SARS-CoV-2 infection.Main Outcomes and Measures: PASC and 44 participant-reported symptoms (with severity thresholds).Results: A total of 9764 participants (89% SARS-CoV-2 infected; 71% female; 16% Hispanic/Latino; 15% non-Hispanic Black; median age, 47 years [IQR, 35-60]) met selection criteria. Adjusted odds ratios were 1.5 or greater (infected vs uninfected participants) for 37 symptoms. Symptoms contributing to PASC score included postexertional malaise, fatigue, brain fog, dizziness, gastrointestinal symptoms, palpitations, changes in sexual desire or capacity, loss of or change in smell or taste, thirst, chronic cough, chest pain, and abnormal movements. Among 2231 participants first infected on or after December 1, 2021, and enrolled within 30 days of infection, 224 (10% [95% CI, 8.8%-11%]) were PASC positive at 6 months.Conclusions and Relevance: A definition of PASC was developed based on symptoms in a prospective cohort study. As a first step to providing a framework for other investigations, iterative refinement that further incorporates other clinical features is needed to support actionable definitions of PASC.

    View details for DOI 10.1001/jama.2023.8823

    View details for PubMedID 37278994

  • Using a 29-mRNA Host Response Classifier To Detect Bacterial Coinfections and Predict Outcomes in COVID-19 Patients Presenting to the Emergency Department. Microbiology spectrum Ram-Mohan, N., Rogers, A. J., Blish, C. A., Nadeau, K. C., Zudock, E. J., Kim, D., Quinn, J. V., Sun, L., Liesenfeld, O., Yang, S. 2022: e0230522


    Clinicians in the emergency department (ED) face challenges in concurrently assessing patients with suspected COVID-19 infection, detecting bacterial coinfection, and determining illness severity since current practices require separate workflows. Here, we explore the accuracy of the IMX-BVN-3/IMX-SEV-3 29 mRNA host response classifiers in simultaneously detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and bacterial coinfections and predicting clinical severity of COVID-19. A total of 161 patients with PCR-confirmed COVID-19 (52.2% female; median age, 50.0 years; 51% hospitalized; 5.6% deaths) were enrolled at the Stanford Hospital ED. RNA was extracted (2.5 mL whole blood in PAXgene blood RNA), and 29 host mRNAs in response to the infection were quantified using Nanostring nCounter. The IMX-BVN-3 classifier identified SARS-CoV-2 infection in 151 patients with a sensitivity of 93.8%. Six of 10 patients undetected by the classifier had positive COVID tests more than 9 days prior to enrollment, and the remaining patients oscillated between positive and negative results in subsequent tests. The classifier also predicted that 6 (3.7%) patients had a bacterial coinfection. Clinical adjudication confirmed that 5/6 (83.3%) of the patients had bacterial infections, i.e., Clostridioides difficile colitis (n = 1), urinary tract infection (n = 1), and clinically diagnosed bacterial infections (n = 3), for a specificity of 99.4%. Two of 101 (2.8%) patients in the IMX-SEV-3 "Low" severity classification and 7/60 (11.7%) in the "Moderate" severity classification died within 30 days of enrollment. IMX-BVN-3/IMX-SEV-3 classifiers accurately identified patients with COVID-19 and bacterial coinfections and predicted patients' risk of death. A point-of-care version of these classifiers, under development, could improve ED patient management, including more accurate treatment decisions and optimized resource utilization. IMPORTANCE We assay the utility of the single-test IMX-BVN-3/IMX-SEV-3 classifiers that require just 2.5 mL of patient blood in concurrently detecting viral and bacterial infections as well as predicting the severity and 30-day outcome from the infection. A point-of-care device, in development, will circumvent the need for blood culturing and drastically reduce the time needed to detect an infection. This will negate the need for empirical use of broad-spectrum antibiotics and allow for antibiotic use stewardship. Additionally, accurate classification of the severity of infection and the prediction of 30-day severe outcomes will allow for appropriate allocation of hospital resources.

    View details for DOI 10.1128/spectrum.02305-22

    View details for PubMedID 36250865

  • Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy. Nature communications Parikh, V. N., Ioannidis, A. G., Jimenez-Morales, D., Gorzynski, J. E., De Jong, H. N., Liu, X., Roque, J., Cepeda-Espinoza, V. P., Osoegawa, K., Hughes, C., Sutton, S. C., Youlton, N., Joshi, R., Amar, D., Tanigawa, Y., Russo, D., Wong, J., Lauzon, J. T., Edelson, J., Mas Montserrat, D., Kwon, Y., Rubinacci, S., Delaneau, O., Cappello, L., Kim, J., Shoura, M. J., Raja, A. N., Watson, N., Hammond, N., Spiteri, E., Mallempati, K. C., Montero-Martín, G., Christle, J., Kim, J., Kirillova, A., Seo, K., Huang, Y., Zhao, C., Moreno-Grau, S., Hershman, S. G., Dalton, K. P., Zhen, J., Kamm, J., Bhatt, K. D., Isakova, A., Morri, M., Ranganath, T., Blish, C. A., Rogers, A. J., Nadeau, K., Yang, S., Blomkalns, A., O'Hara, R., Neff, N. F., DeBoever, C., Szalma, S., Wheeler, M. T., Gates, C. M., Farh, K., Schroth, G. P., Febbo, P., deSouza, F., Cornejo, O. E., Fernandez-Vina, M., Kistler, A., Palacios, J. A., Pinsky, B. A., Bustamante, C. D., Rivas, M. A., Ashley, E. A. 2022; 13 (1): 5107


    The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.

    View details for DOI 10.1038/s41467-022-32397-8

    View details for PubMedID 36042219

  • Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. EBioMedicine Ozonoff, A., Schaenman, J., Jayavelu, N. D., Milliren, C. E., Calfee, C. S., Cairns, C. B., Kraft, M., Baden, L. R., Shaw, A. C., Krammer, F., van Bakel, H., Esserman, D. A., Liu, S., Sesma, A. F., Simon, V., Hafler, D. A., Montgomery, R. R., Kleinstein, S. H., Levy, O., Bime, C., Haddad, E. K., Erle, D. J., Pulendran, B., Nadeau, K. C., Davis, M. M., Hough, C. L., Messer, W. B., Higuita, N. I., Metcalf, J. P., Atkinson, M. A., Brakenridge, S. C., Corry, D., Kheradmand, F., Ehrlich, L. I., Melamed, E., McComsey, G. A., Sekaly, R., Diray-Arce, J., Peters, B., Augustine, A. D., Reed, E. F., Altman, M. C., Becker, P. M., Rouphael, N. 2022; 83: 104208


    Better understanding of the association between characteristics of patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management.Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective, observational study of 1164 patients from 20 hospitals across the United States. Disease severity was assessed using a 7-point ordinal scale based on degree of respiratory illness. Patients were prospectively surveyed for 1 year after discharge for post-acute sequalae of COVID-19 (PASC) through quarterly surveys. Demographics, comorbidities, radiographic findings, clinical laboratory values, SARS-CoV-2 PCR and serology were captured over a 28-day period. Multivariable logistic regression was performed.The median age was 59 years (interquartile range [IQR] 20); 711 (61%) were men; overall mortality was 14%, and 228 (20%) required invasive mechanical ventilation. Unsupervised clustering of ordinal score over time revealed distinct disease course trajectories. Risk factors associated with prolonged hospitalization or death by day 28 included age ≥ 65 years (odds ratio [OR], 2.01; 95% CI 1.28-3.17), Hispanic ethnicity (OR, 1.71; 95% CI 1.13-2.57), elevated baseline creatinine (OR 2.80; 95% CI 1.63- 4.80) or troponin (OR 1.89; 95% 1.03-3.47), baseline lymphopenia (OR 2.19; 95% CI 1.61-2.97), presence of infiltrate by chest imaging (OR 3.16; 95% CI 1.96-5.10), and high SARS-CoV2 viral load (OR 1.53; 95% CI 1.17-2.00). Fatal cases had the lowest ratio of SARS-CoV-2 antibody to viral load levels compared to other trajectories over time (p=0.001). 589 survivors (51%) completed at least one survey at follow-up with 305 (52%) having at least one symptom consistent with PASC, most commonly dyspnea (56% among symptomatic patients). Female sex was the only associated risk factor for PASC.Integration of PCR cycle threshold, and antibody values with demographics, comorbidities, and laboratory/radiographic findings identified risk factors for 28-day outcome severity, though only female sex was associated with PASC. Longitudinal clinical phenotyping offers important insights, and provides a framework for immunophenotyping for acute and long COVID-19.NIH.

    View details for DOI 10.1016/j.ebiom.2022.104208

    View details for PubMedID 35952496

  • Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post-COVID-19 syndrome. JCI insight Jia, X., Cao, S., Lee, A. S., Manohar, M., Sindher, S. B., Ahuja, N., Artandi, M., Blish, C. A., Blomkalns, A. L., Chang, I., Collins, W. J., Desai, M., Din, H. N., Do, E., Fernandes, A., Geng, L. N., Rosenberg-Hasson, Y., Mahoney, M. R., Glascock, A. L., Chan, L. Y., Fong, S. Y., Phelps, M., Raeber, O., Purington, N., Röltgen, K., Rogers, A. J., Snow, T., Wang, T. T., Solis, D., Vaughan, L., Verghese, M., Maecker, H., Wittman, R., Puri, R., Kistler, A., Yang, S., Boyd, S. D., Pinsky, B. A., Chinthrajah, S., Nadeau, K. C. 2022; 7 (13)


    BACKGROUNDProlonged symptoms after SARS-CoV-2 infection are well documented. However, which factors influence development of long-term symptoms, how symptoms vary across ethnic groups, and whether long-term symptoms correlate with biomarkers are points that remain elusive.METHODSAdult SARS-CoV-2 reverse transcription PCR-positive (RT-PCR-positive) patients were recruited at Stanford from March 2020 to February 2021. Study participants were seen for in-person visits at diagnosis and every 1-3 months for up to 1 year after diagnosis; they completed symptom surveys and underwent blood draws and nasal swab collections at each visit.RESULTSOur cohort (n = 617) ranged from asymptomatic to critical COVID-19 infections. In total, 40% of participants reported at least 1 symptom associated with COVID-19 six months after diagnosis. Median time from diagnosis to first resolution of all symptoms was 44 days; median time from diagnosis to sustained symptom resolution with no recurring symptoms for 1 month or longer was 214 days. Anti-nucleocapsid IgG level in the first week after positive RT-PCR test and history of lung disease were associated with time to sustained symptom resolution. COVID-19 disease severity, ethnicity, age, sex, and remdesivir use did not affect time to sustained symptom resolution.CONCLUSIONWe found that all disease severities had a similar risk of developing post-COVID-19 syndrome in an ethnically diverse population. Comorbid lung disease and lower levels of initial IgG response to SARS-CoV-2 nucleocapsid antigen were associated with longer symptom duration.TRIAL, NCT04373148.FUNDINGNIH UL1TR003142 CTSA grant, NIH U54CA260517 grant, NIEHS R21 ES03304901, Sean N Parker Center for Allergy and Asthma Research at Stanford University, Chan Zuckerberg Biohub, Chan Zuckerberg Initiative, Sunshine Foundation, Crown Foundation, and Parker Foundation.

    View details for DOI 10.1172/jci.insight.156713

    View details for PubMedID 35801588

  • Biochemical, biophysical, and immunological characterization of respiratory secretions in severe SARS-CoV-2 infections. JCI insight Kratochvil, M. J., Kaber, G., Demirdjian, S., Cai, P. C., Burgener, E. B., Nagy, N., Barlow, G. L., Popescu, M., Nicolls, M. R., Ozawa, M. G., Regula, D. P., Pacheco-Navarro, A. E., Yang, S., de Jesus Perez, V. A., Karmouty-Quintana, H., Peters, A. M., Zhao, B., Buja, M. L., Johnson, P. Y., Vernon, R. B., Wight, T. N., Stanford COVID-19 Biobank Study Group, Milla, C. E., Rogers, A. J., Spakowitz, A. J., Heilshorn, S. C., Bollyky, P. L. 2022; 7 (12)


    Thick, viscous respiratory secretions are a major pathogenic feature of COVID-19, but the composition and physical properties of these secretions are poorly understood. We characterized the composition and rheological properties (i.e., resistance to flow) of respiratory secretions collected from intubated COVID-19 patients. We found the percentages of solids and protein content were greatly elevated in COVID-19 compared with heathy control samples and closely resembled levels seen in cystic fibrosis, a genetic disease known for thick, tenacious respiratory secretions. DNA and hyaluronan (HA) were major components of respiratory secretions in COVID-19 and were likewise abundant in cadaveric lung tissues from these patients. COVID-19 secretions exhibited heterogeneous rheological behaviors, with thicker samples showing increased sensitivity to DNase and hyaluronidase treatment. In histologic sections from these same patients, we observed increased accumulation of HA and the hyaladherin versican but reduced tumor necrosis factor-stimulated gene-6 staining, consistent with the inflammatory nature of these secretions. Finally, we observed diminished type I interferon and enhanced inflammatory cytokines in these secretions. Overall, our studies indicated that increases in HA and DNA in COVID-19 respiratory secretion samples correlated with enhanced inflammatory burden and suggested that DNA and HA may be viable therapeutic targets in COVID-19 infection.

    View details for DOI 10.1172/jci.insight.152629

    View details for PubMedID 35730564

  • Origin of novel coronavirus causing COVID-19: A computational biology study using artificial intelligence. Machine learning with applications Nguyen, T. T., Abdelrazek, M., Nguyen, D. T., Aryal, S., Nguyen, D. T., Reddy, S., Nguyen, Q. V., Khatami, A., Nguyen, T. T., Hsu, E. B., Yang, S. 2022: 100328


    Origin of the COVID-19 virus (SARS-CoV-2) has been intensely debated in the scientific community since the first infected cases were detected in December 2019. The disease has caused a global pandemic, leading to deaths of thousands of people across the world and thus finding origin of this novel coronavirus is important in responding and controlling the pandemic. Recent research results suggest that bats or pangolins might be the hosts for SARS-CoV-2 based on comparative studies using its genomic sequences. This paper investigates the SARS-CoV-2 origin by using artificial intelligence (AI)-based unsupervised learning algorithms and raw genomic sequences of the virus. More than 300 genome sequences of COVID-19 infected cases collected from different countries are explored and analysed using unsupervised clustering methods. The results obtained from various AI-enabled experiments using clustering algorithms demonstrate that all examined SARS-CoV-2 genomes belong to a cluster that also contains bat and pangolin coronavirus genomes. This provides evidence strongly supporting scientific hypotheses that bats and pangolins are probable hosts for SARS-CoV-2. At the whole genome analysis level, our findings also indicate that bats are more likely the hosts for the COVID-19 virus than pangolins.

    View details for DOI 10.1016/j.mlwa.2022.100328

    View details for PubMedID 35599960

  • Diagnosis of Bloodstream Infections: An Evolution of Technologies towards Accurate and Rapid Identification and Antibiotic Susceptibility Testing. Antibiotics (Basel, Switzerland) Tjandra, K. C., Ram-Mohan, N., Abe, R., Hashemi, M. M., Lee, J., Chin, S. M., Roshardt, M. A., Liao, J. C., Wong, P. K., Yang, S. 2022; 11 (4)


    Bloodstream infections (BSI) are a leading cause of death worldwide. The lack of timely and reliable diagnostic practices is an ongoing issue for managing BSI. The current gold standard blood culture practice for pathogen identification and antibiotic susceptibility testing is time-consuming. Delayed diagnosis warrants the use of empirical antibiotics, which could lead to poor patient outcomes, and risks the development of antibiotic resistance. Hence, novel techniques that could offer accurate and timely diagnosis and susceptibility testing are urgently needed. This review focuses on BSI and highlights both the progress and shortcomings of its current diagnosis. We surveyed clinical workflows that employ recently approved technologies and showed that, while offering improved sensitivity and selectivity, these techniques are still unable to deliver a timely result. We then discuss a number of emerging technologies that have the potential to shorten the overall turnaround time of BSI diagnosis through direct testing from whole blood-while maintaining, if not improving-the current assay's sensitivity and pathogen coverage. We concluded by providing our assessment of potential future directions for accelerating BSI pathogen identification and the antibiotic susceptibility test. While engineering solutions have enabled faster assay turnaround, further progress is still needed to supplant blood culture practice and guide appropriate antibiotic administration for BSI patients.

    View details for DOI 10.3390/antibiotics11040511

    View details for PubMedID 35453262

  • Association Between SARS-CoV-2 RNAemia and Postacute Sequelae of COVID-19. Open forum infectious diseases Ram-Mohan, N., Kim, D., Rogers, A. J., Blish, C. A., Nadeau, K. C., Blomkalns, A. L., Yang, S. 2022; 9 (2): ofab646


    Determinants of Post-Acute Sequelae of COVID-19 are not known. Here we show that 83.3% of patients with viral RNA in blood (RNAemia) at presentation were symptomatic in the post-acute phase. RNAemia at presentation successfully predicted PASC, independent of patient demographics, worst disease severity, and length of symptoms.

    View details for DOI 10.1093/ofid/ofab646

    View details for PubMedID 35111870

    View details for PubMedCentralID PMC8802799

  • A vacuum-assisted, highly parallelized microfluidic array for performing multi-step digital assays LAB ON A CHIP Hu, J., Chen, L., Zhang, P., Hsieh, K., Li, H., Yang, S., Wang, T. 2021; 21 (23): 4716-4724


    There remains an unmet need for a simple microfluidic platform that can perform multi-step and multi-reagent biochemical assays in parallel for high-throughput detection and analysis of single molecules and single cells. In response, we report herein a PDMS-based vacuum-driven microfluidic array that is capable of multi-step sample loading and digitalization. The array features multi-level bifurcation microchannels connecting to 4096 dead-end microchambers for partitioning liquid reagents/samples. To realize multi-step repetitive liquid sample loading, we attach an external vacuum onto the chip to create internal negative pressure for a continuous liquid driving force. We demonstrated a high uniformity of our device for three sequential liquid loadings. To further improve its utility, we developed a thermosetting-oil covering method to prevent evaporation for assays that require high temperatures. We successfully performed digital PCR assays on our device, demonstrating the efficient multi-step reagent handling and the effective anti-evaporation design for thermal cycling. Furthermore, we performed a digital PCR detection for single-cell methicillin-resistant Staphylococcus aureus using a three-step loading approach and achieved accurate single-cell quantification. Taken together, we have demonstrated that our vacuum-driven microfluidic array is capable of multi-step sample digitalization at high throughput for single-molecule and single-cell analyses.

    View details for DOI 10.1039/d1lc00636c

    View details for Web of Science ID 000718420300001

    View details for PubMedID 34779472

  • Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. The Journal of experimental medicine Wilk, A. J., Lee, M. J., Wei, B., Parks, B., Pi, R., Martinez-Colon, G. J., Ranganath, T., Zhao, N. Q., Taylor, S., Becker, W., Stanford COVID-19 Biobank, Jimenez-Morales, D., Blomkalns, A. L., O'Hara, R., Ashley, E. A., Nadeau, K. C., Yang, S., Holmes, S., Rabinovitch, M., Rogers, A. J., Greenleaf, W. J., Blish, C. A. 2021; 218 (8)


    Our understanding of protective versus pathological immune responses to SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses revealed widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, including prominent hyperactivation signatures in neutrophils and NK cells. We also identified chromatin accessibility changes at NF-kappaB binding sites within cytokine gene loci as a potential mechanism for the striking lack of pro-inflammatory cytokine production observed in monocytes in severe and fatal COVID-19. We further demonstrated that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity-associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.

    View details for DOI 10.1084/jem.20210582

    View details for PubMedID 34128959

  • Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19. ACS central science Delaveris, C. S., Wilk, A. J., Riley, N. M., Stark, J. C., Yang, S. S., Rogers, A. J., Ranganath, T., Nadeau, K. C., Blish, C. A., Bertozzi, C. R. 2021; 7 (4): 650-657


    Severe cases of coronavirus disease 2019 (COVID-19), caused by infection with SARS-CoV-2, are characterized by a hyperinflammatory immune response that leads to numerous complications. Production of proinflammatory neutrophil extracellular traps (NETs) has been suggested to be a key factor in inducing a hyperinflammatory signaling cascade, allegedly causing both pulmonary tissue damage and peripheral inflammation. Accordingly, therapeutic blockage of neutrophil activation and NETosis, the cell death pathway accompanying NET formation, could limit respiratory damage and death from severe COVID-19. Here, we demonstrate that synthetic glycopolymers that activate signaling of the neutrophil checkpoint receptor Siglec-9 suppress NETosis induced by agonists of viral toll-like receptors (TLRs) and plasma from patients with severe COVID-19. Thus, Siglec-9 agonism is a promising therapeutic strategy to curb neutrophilic hyperinflammation in COVID-19.

    View details for DOI 10.1021/acscentsci.0c01669

    View details for PubMedID 34056095

    View details for PubMedCentralID PMC8009098

  • SARS-CoV-2 IgG Seropositivity and Acute Asymptomatic Infection Rate Among Firefighter First Responders in an Early Outbreak County in California. Prehospital emergency care : official journal of the National Association of EMS Physicians and the National Association of State EMS Directors Newberry, J. A., Gautreau, M., Staats, K., Carrillo, E., Mulkerin, W., Yang, S., Kohn, M. A., Matheson, L., Boyd, S. D., Pinsky, B. A., Blomkalns, A. L., Strehlow, M. C., D'Souza, P. A. 2021: 1–10


    Objective: Firefighter first responders and other emergency medical services (EMS) personnel have been among the highest risk healthcare workers for illness during the SARS-CoV-2 pandemic. We sought to determine the rate of seropositivity for SARS-CoV-2 IgG antibodies and of acute asymptomatic infection among firefighter first responders in a single county with early exposure in the pandemic.Methods: We conducted a cross-sectional study of clinically active firefighters cross-trained as paramedics or EMTs in the fire departments of Santa Clara County, California. Firefighters without current symptoms were tested between June and August 2020. Our primary outcomes were rates of SARS-CoV-2 IgG antibody seropositivity and SARS-CoV-2 RT-PCR swab positivity for acute infection. We report cumulative incidence, participant characteristics with frequencies and proportions, and proportion positive and associated relative risk (with 95% confidence intervals).Results: We enrolled 983 out of 1339 eligible participants (response rate: 73.4%). Twenty-five participants (2.54%, 95% CI 1.65-3.73) tested positive for IgG antibodies and 9 (0.92%, 95% CI 0.42-1.73) tested positive for SARS-CoV-2 by RT-PCR. Our cumulative incidence, inclusive of self-reported prior positive PCR tests, was 34 (3.46%, 95% CI 2.41-4.80).Conclusion: In a county with one of the earliest outbreaks in the United States, the seroprevalence among firefighter first responders was lower than that reported by other studies of frontline health care workers, while the cumulative incidence remained higher than that seen in the surrounding community.

    View details for DOI 10.1080/10903127.2021.1912227

    View details for PubMedID 33819128

  • A Novel Platform Using RNA Signatures To Accelerate Antimicrobial Susceptibility Testing in Neisseria gonorrhoeae (vol 58, e01152-20, 2020) JOURNAL OF CLINICAL MICROBIOLOGY Hashemi, M. M., Ram-Mohan, N., Yang, X., Andini, N., Gessner, N. R., Carroll, K. C., Wang, T., Yang, S. 2021; 59 (3)
  • A Rapid Single-Cell Antimicrobial Susceptibility Testing Workflow for Bloodstream Infections. Biosensors Forsyth, B., Torab, P., Lee, J. H., Malcom, T., Wang, T. H., Liao, J. C., Yang, S., Kvam, E., Puleo, C., Wong, P. K. 2021; 11 (8)


    Bloodstream infections are a significant cause of morbidity and mortality worldwide. The rapid initiation of effective antibiotic treatment is critical for patients with bloodstream infections. However, the diagnosis of bloodborne pathogens is largely complicated by the matrix effect of blood and the lengthy blood tube culture procedure. Here we report a culture-free workflow for the rapid isolation and enrichment of bacterial pathogens from whole blood for single-cell antimicrobial susceptibility testing (AST). A dextran sedimentation step reduces the concentration of blood cells by 4 orders of magnitude in 20-30 min while maintaining the effective concentration of bacteria in the sample. Red blood cell depletion facilitates the downstream centrifugation-based enrichment step at a sepsis-relevant bacteria concentration. The workflow is compatible with common antibiotic-resistant bacteria and does not influence the minimum inhibitory concentrations. By applying a microfluidic single-cell trapping device, we demonstrate the workflow for the rapid determination of bacterial infection and antimicrobial susceptibility testing at the single-cell level. The entire workflow from blood to categorical AST result can be completed in less than two hours.

    View details for DOI 10.3390/bios11080288

    View details for PubMedID 34436090

  • A Perspective on the Role of Point-of-Care "Immuno-Triaging" to Optimize COVID-19 Vaccination Distribution in a Time of Scarcity. Frontiers in public health Zhang, Y., Rogers, A., Nadeau, K., Gu, J., Yang, S. 2021; 9: 638316


    Vaccine bears hope to bring COVID-19 pandemic under control. With limited supply, vaccines must be utilized efficiently to provide protection to those who need it most. Currently, no practical framework has been proposed to ensure fair vaccine allocation at individual level, which is a recognized problem. We propose here an evidence-based decision-making framework for COVID-19 vaccine appropriation that prioritizes vaccine doses to individuals based on their immunological status, or immuno-triaging. To ensure successful implementation of the proposed framework, point-of-care (POC) immunodiagnostic testing is needed to quickly ramp up the testing capability. Considerations for deploying POC immunodiagnostic testing at such a large scale are discussed. We hope that the proposed immunological decision-making framework for evidence-based COVID-19 vaccine appropriation provides an objective approach to ensure fair and efficient utilization of the scarce vaccine resource at the individual level that also maximizes the collective societal benefit.

    View details for DOI 10.3389/fpubh.2021.638316

    View details for PubMedID 34414149

  • A novel platform to accelerate antimicrobial susceptibility testing in Neisseria gonorrhoeae using RNA signatures. Journal of clinical microbiology Hashemi, M. M., Ram-Mohan, N., Yang, X., Andini, N., Gessner, N. R., Carroll, K. C., Wang, T., Yang, S. 2020


    The rise of antimicrobial-resistant pathogens can be attributed to the lack of a rapid pathogen identification (ID) or antimicrobial susceptibility testing (AST), resulting in delayed therapeutic decisions at the point-of-care. Gonorrhea is usually empirically treated with no AST results available before treatment, thus contributing to the rapid rise in drug resistance. Herein we present a rapid AST platform using RNA signatures for Neisseria gonorrhoeae (NG). RNA-seq followed by bioinformatic tools were applied to explore potential markers in the transcriptome profile of NG upon minutes of azithromycin exposure. Validation of candidate markers using qRT-PCR showed that two markers (arsR (NGO1562) and rpsO) can deliver accurate AST results across 14 tested isolates. Further validation of our susceptibility threshold in comparison to MIC across 64 more isolates confirmed the reliability of our platform. Our RNA markers combined with emerging molecular point-of-care systems has the potential to greatly accelerate both ID and AST to inform treatment.

    View details for DOI 10.1128/JCM.01152-20

    View details for PubMedID 32967905

  • RNA markers for ultra-rapid molecular antimicrobial susceptibility testing in fluoroquinolone-treated Klebsiella pneumoniae Journal of Antimicrobial Chemotherapy Yang, X., Hashemi, M. M., Andini, N., Li, M. M., Kuang, S., Carroll, K. C., Wang, T., Yang, S. 2020

    View details for DOI 10.1093/jac/dkaa078

  • A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections BIOTECHNOLOGY ADVANCES Zhang, Y., Hu, A., Andini, N., Yang, S. 2019; 37 (3): 476–90
  • Emerging Analytical Techniques for Rapid Pathogen Identification and Susceptibility Testing. Annual review of analytical chemistry (Palo Alto, Calif.) Shin, D. J., Andini, N., Hsieh, K., Yang, S., Wang, T. 2019


    In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recent developments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays. Expected final online publication date for the Annual Review of Analytical Chemistry Volume 12 is June 12, 2019. Please see for revised estimates.

    View details for PubMedID 30939033

  • Nanoarray Digital Polymerase Chain Reaction with High-Resolution Melt for Enabling Broad Bacteria Identification and Pheno-Molecular Antimicrobial Susceptibility Test. Analytical chemistry Athamanolap, P. n., Hsieh, K. n., O'Keefe, C. M., Zhang, Y. n., Yang, S. n., Wang, T. H. 2019; 91 (20): 12784–92


    Toward combating infectious diseases caused by pathogenic bacteria, there remains an unmet need for diagnostic tools that can broadly identify the causative bacteria and determine their antimicrobial susceptibilities from complex and even polymicrobial samples in a timely manner. To address this need, a microfluidic and machine-learning-based platform that performs broad bacteria identification (ID) and rapid yet reliable antimicrobial susceptibility testing (AST) is developed. Specifically, this platform builds on "pheno-molecular AST", a strategy that transforms nucleic acid amplification tests (NAATs) into phenotypic AST through quantitative detection of bacterial genomic replication, and utilizes digital polymerase chain reaction (PCR) and digital high-resolution melt (HRM) to quantify and identify bacterial DNA molecules. Bacterial species are identified using integrated experiment-machine learning algorithm via HRM profiles. Digital DNA quantification allows for rapid growth measurement that reflects susceptibility profiles of each bacterial species within only 30 min of antibiotic exposure. As a demonstration, multiple bacterial species and their susceptibility profiles in a spiked-in polymicrobial urine specimen were correctly identified with a total turnaround time of ∼4 h. With further development and clinical validation, this platform holds the potential for improving clinical diagnostics and enabling targeted antibiotic treatments.

    View details for DOI 10.1021/acs.analchem.9b02344

    View details for PubMedID 31525952

  • Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity Nature Immunology Liu, Q., Johnson, E., et al 2019
  • Using a novel rapid viral test to improve triage of emergency department patients with acute respiratory illness during flu season JOURNAL OF CLINICAL VIROLOGY Pedersen, C. J., Rogan, D. T., Yang, S., Quinn, J. 2018; 108: 72-76
  • Using a novel rapid viral test to improve triage of emergency department patients with acute respiratory illness during flu season. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology Pedersen, C. J., Rogan, D. T., Yang, S., Quinn, J. V. 2018; 108: 72–76


    BACKGROUND: Acute respiratory illnesses (ARI) are mostly viral in etiology and cause significant morbidity and mortality. Point of care PCR (POC-PCR) is a promising new technology for rapid virus identification but utility in the Emergency Department (ED) is not yet defined.OBJECTIVES: Primarily, to investigate the value of POC-PCR in rapidly identifying RSV and influenza in the setting of ED triage. Additionally, to assess whether rapid knowledge of accurate test results would improve patient management by preventing nosocomial transmission and optimizing the prescription of antimicrobials for ARIs.STUDY DESIGN: A prospective cohort study of consecutive ED patients with ARI symptoms during peak flu season was conducted. Patient nasopharyngeal swabs were collected and tested using a POC-PCR device; physicians and patients were blinded to results. Virus positive and negative groups were compared by ED patient room placement and antimicrobial therapy ordered. Specificity and sensitivity were calculated using laboratory-PCR as the gold standard.RESULTS: Of 119 participants, 52.9% were POC-PCR positive - Influenza A (42.9%), RSV (41.3%), influenza B (15.9%). Nearly 70% of virus positive patients were placed rooms shared with non-ARI patients. Antibiotics were prescribed for 27.3% of virus positive patients, and 77.8% of oseltamivir-eligible patients did not receive therapy. POC-PCR was 100% sensitive (95% CI, 80.5-100.0%) and 95.2% specific (95% CI, 76.2-99.9%).CONCLUSIONS: Rapid POC-PCR for influenza and RSV in ED triage has excellent sensitivity and specificity and the potential to improve social distancing practices through better triage and increase appropriate prescription of antimicrobials.

    View details for PubMedID 30261422

  • A review on cluster estimation methods and their application to neural spike data JOURNAL OF NEURAL ENGINEERING Zhang, J., Thanh Nguyen, Cogill, S., Bhatti, A., Luo, L., Yang, S., Nahavandi, S. 2018; 15 (3): 031003


    The extracellular action potentials recorded on an electrode result from the collective simultaneous electrophysiological activity of an unknown number of neurons. Identifying and assigning these action potentials to their firing neurons-'spike sorting'-is an indispensable step in studying the function and the response of an individual or ensemble of neurons to certain stimuli. Given the task of neural spike sorting, the determination of the number of clusters (neurons) is arguably the most difficult and challenging issue, due to the existence of background noise and the overlap and interactions among neurons in neighbouring regions. It is not surprising that some researchers still rely on visual inspection by experts to estimate the number of clusters in neural spike sorting. Manual inspection, however, is not suitable to processing the vast, ever-growing amount of neural data. To address this pressing need, in this paper, thirty-three clustering validity indices have been comprehensively reviewed and implemented to determine the number of clusters in neural datasets. To gauge the suitability of the indices to neural spike data, and inform the selection process, we then calculated the indices by applying k-means clustering to twenty widely used synthetic neural datasets and one empirical dataset, and compared the performance of these indices against pre-existing ground truth labels. The results showed that the top five validity indices work consistently well across variations in noise level, both for the synthetic datasets and the real dataset. Using these top performing indices provides strong support for the determination of the number of neural clusters, which is essential in the spike sorting process.

    View details for DOI 10.1088/1741-2552/aab385

    View details for Web of Science ID 000430324400001

    View details for PubMedID 29498353

  • Impact of Rapid Molecular Respiratory Virus Testing on Real-Time Decision Making in a Pediatric Emergency Department JOURNAL OF MOLECULAR DIAGNOSTICS Rogan, D. T., Kochar, M. S., Yang, S., Quinn, J. V. 2017; 19 (3): 460-467


    Acute respiratory illnesses (ARIs) are usually viral [influenza, respiratory syncytial virus (RSV)] and account for 25% of emergency department (ED) peak-season visits. Laboratory PCR testing is accurate albeit slow, whereas rapid antigen testing is inaccurate. We determined the impact of bedside PCR (molecular point-of-care test; mPOCT) on pediatric ARI management. This was a prospective cohort study of consecutive pediatric patients with ED-ordered respiratory PCR test, enrolled over 9 weeks during peak flu season. On ordering, ED physicians were interviewed to ascertain real-time plans if given immediate influenza/RSV PCR results for the current patient. Two groups were compared: actual management and management adjusted for mPOCT results. We compared ED length of stay (LOS), tests ordered, and antibiotic/antiviral ordering. One-hundred thirty-six respiratory PCR panels were ordered, 71 by admitting team, 61 for ED management. Of 61 ED-initiated tests, physicians indicated in 39 cases (64%) they would change patient management were bedside viral results available. Physicians would have decreased ED LOS by 33 minutes, ordered fewer tests (18%; P < 0.001) with average patient charge savings of $669, fewer antibiotics among discharged patients (17%; P = 0.043), and increased appropriate antiviral use (13%; P = 0.023). Rapid bedside ARI mPOCT PCR has the potential to decrease ED LOS, reduce diagnostic tests and patient charges, and increase appropriate use of antibiotics and antiviral agents.

    View details for DOI 10.1016/j.jmoldx.2017.01.009

    View details for Web of Science ID 000400314100011

    View details for PubMedID 28341587

    View details for PubMedCentralID PMC5417039

  • Microbial Typing by Machine Learned DNA Melt Signatures SCIENTIFIC REPORTS Andini, N., Wang, B., Athamanolap, P., Hardick, J., Masek, B. J., Thair, S., Hu, A., Avornu, G., Peterson, S., Cogill, S., Rothman, R. E., Carroll, K. C., Gaydos, C. A., Wang, J. T., Batzoglou, S., Yang, S. 2017; 7


    There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.

    View details for DOI 10.1038/srep42097

    View details for Web of Science ID 000393494300001

    View details for PubMedID 28165067

  • Umbilical Cord Blood NOS1 as a Potential Biomarker of Neonatal Encephalopathy. Frontiers in pediatrics Lei, J. n., Paules, C. n., Nigrini, E. n., Rosenzweig, J. M., Bahabry, R. n., Farzin, A. n., Yang, S. n., Northington, F. J., Oros, D. n., McKenney, S. n., Johnston, M. V., Graham, E. M., Burd, I. n. 2017; 5: 112


    There are no definitive markers to aid in diagnosis of neonatal encephalopathy (NE). The purpose of our study was (1) to identify and evaluate the utility of neuronal nitric oxide synthase (NOS1) in umbilical cord blood as a NE biomarker and (2) to identify the source of NOS1 in umbilical cord blood.This was a nested case-control study of neonates >35 weeks of gestation. ELISA for NOS1 in umbilical cord blood was performed. Sources of NOS1 in umbilical cord were investigated by immunohistochemistry, western blot, ELISA, and quantitative PCR. Furthermore, umbilical cords of full-term neonates were subjected to 1% hypoxia ex vivo.NOS1 was present in umbilical cord blood and increased in NE cases compared with controls. NOS1 was expressed in endothelial cells of the umbilical cord vein, but not in artery or blood cells. In ex vivo experiments, hypoxia was associated with increased levels of NOS1 in venous endothelial cells of the umbilical cord as well as in ex vivo culture medium.This is the first study to investigate an early marker of NE. NOS1 is elevated with hypoxia, and further studies are needed to investigate it as a valuable tool for early diagnosis of neonatal brain injury.

    View details for DOI 10.3389/fped.2017.00112

    View details for PubMedID 28649562

    View details for PubMedCentralID PMC5466059

  • Integrated Bacterial Identification and Antimicrobial Susceptibility Testing Using PCR and High-Resolution Melt. Analytical chemistry Athamanolap, P. n., Hsieh, K. n., Chen, L. n., Yang, S. n., Wang, T. H. 2017


    Accurate and timely diagnostics are critical for managing bacterial infections. The current gold standard, culture-based diagnostics, can provide clinicians with comprehensive diagnostic information including bacterial identity and antimicrobial susceptibility, but they often require several days of turnaround time, which leads to compromised clinical outcome and promotes the spread of antibiotic resistance. Nucleic acid amplification tests such as PCR have significantly accelerated the detection of specific bacteria but generally lack the capacities for broad-based bacterial identification or antimicrobial susceptibility testing. Here, we report an integrated assay based on PCR and high-resolution melt (HRM) for rapid diagnosis for bacterial infections. In our assay, we measure bacterial growth in the presence or absence of certain antibiotics with real-time quantitative PCR or digital PCR to determine antimicrobial susceptibility. In addition, we use HRM and a machine learning algorithm to identify bacterial species based on melt-curve profiles of the 16S rRNA gene in an automated fashion. As a demonstration, we correctly identified the bacterial species and their antimicrobial susceptibility profiles for multiple unknown samples in blinded tests within ∼6.5 h.

    View details for PubMedID 29027789

  • RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process PLOS ONE Thanh Nguyen, T., Bhatti, A., Yang, S., Nahavandi, S. 2016; 11 (10)


    This paper introduces an approach to classification of RNA-seq read counts using grey relational analysis (GRA) and Bayesian Gaussian process (GP) models. Read counts are transformed to microarray-like data to facilitate normal-based statistical methods. GRA is designed to select differentially expressed genes by integrating outcomes of five individual feature selection methods including two-sample t-test, entropy test, Bhattacharyya distance, Wilcoxon test and receiver operating characteristic curve. GRA performs as an aggregate filter method through combining advantages of the individual methods to produce significant feature subsets that are then fed into a nonparametric GP model for classification. The proposed approach is verified by using two benchmark real datasets and the five-fold cross-validation method. Experimental results show the performance dominance of the GRA-based feature selection method as well as GP classifier against their competing methods. Moreover, the results demonstrate that GRA-GP considerably dominates the sparse Poisson linear discriminant analysis classifiers, which were introduced specifically for read counts, on different number of features. The proposed approach therefore can be implemented effectively in real practice for read count data analysis, which is useful in many applications including understanding disease pathogenesis, diagnosis and treatment monitoring at the molecular level.

    View details for DOI 10.1371/journal.pone.0164766

    View details for Web of Science ID 000389602800048

    View details for PubMedID 27783633

    View details for PubMedCentralID PMC5082617

  • Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping SCIENTIFIC REPORTS Fraley, S. I., Athamanolap, P., Masek, B. J., Hardick, J., Carroll, K. C., Hsieh, Y., Rothman, R. E., Gaydos, C. A., Wang, T., Yang, S. 2015
  • A rabbit model of non-typhoidal Salmonella bacteremia COMPARATIVE IMMUNOLOGY MICROBIOLOGY AND INFECTIOUS DISEASES Panda, A., Tatarov, I., Masek, B. J., Hardick, J., Crusan, A., Wakefield, T., Carroll, K., Yang, S., Hsieh, Y., Lipsky, M. M., McLeod, C. G., Levine, M. M., Rothman, R. E., Gaydos, C. A., DeTolla, L. J. 2014; 37 (4): 211-220


    Bacteremia is an important cause of morbidity and mortality in humans. In this study, we focused on the development of an animal model of bacteremia induced by non-typhoidal Salmonella. New Zealand White rabbits were inoculated with a human isolate of non-typhoidal Salmonella strain CVD J73 via the intra-peritoneal route. Blood samples were collected at specific time points and at euthanasia from infected rabbits. Additionally, tissue samples from the heart, lungs, spleen, gastrointestinal tract, liver and kidneys were obtained at euthanasia. All experimentally infected rabbits displayed clinical signs of disease (fever, dehydration, weight loss and lethargy). Tissues collected at necropsy from the animals exhibited histopathological changes indicative of bacteremia. Non-typhoidal Salmonella bacteria were detected in the blood and tissue samples of infected rabbits by microbiological culture and real-time PCR assays. The development of this animal model of bacteremia could prove to be a useful tool for studying how non-typhoidal Salmonella infections disseminate and spread in humans.

    View details for DOI 10.1016/j.cimid.2014.05.004

    View details for Web of Science ID 000343351700002

    View details for PubMedID 25033732

    View details for PubMedCentralID PMC4167468

  • Sensitive Detection and Serovar Differentiation of Typhoidal and Nontyphoidal Salmonella enterica Species Using 16S rRNA Gene PCR Coupled with High-Resolution Melt Analysis JOURNAL OF MOLECULAR DIAGNOSTICS Masek, B. J., Hardick, J., Won, H., Yang, S., Hsieh, Y., Rothman, R. E., Gaydos, C. A. 2014; 16 (2): 261-266


    Salmonella enterica species infections are a significant public health problem causing high morbidity rates worldwide and high mortality rates in the developing world. These infections are not always rapidly diagnosed as a cause of bloodstream infections because of the limitations of blood culture, which greatly affects clinical care as a result of treatment delays. A molecular diagnostic assay that could rapidly detect and identify S. enterica species infections as a cause of sepsis is needed. Nine typhoidal and nontyphoidal S. enterica serovars were used to establish the limit of detection (LOD) of a previously published 16S rRNA gene PCR (16S PCR) in mock whole blood specimens. In addition, 16 typhoidal and nontyphoidal S. enterica serovars were used to evaluate the serovar differentiation capability of 16S PCR coupled with high-resolution melt analysis. The overall LOD of 16S PCR for the nine typhoidal and nontyphoidal S. enterica serovars analyzed was <10 colony-forming units per milliliter (CFU/mL) in mock whole blood specimens, with the lowest and highest LOD at <1 CFU/mL and 9 CFU/mL, respectively. By high-resolution melt analysis, the typhoidal and nontyphoidal S. enterica serovar groups analyzed each generated a unique grouping code, allowing for serovar-level identification. 16S PCR coupled with high-resolution melt analysis could be a useful molecular diagnostic that could enhance the current diagnostic, treatment, and surveillance methods of S. enterica bloodstream infections.

    View details for DOI 10.1016/j.jmoldx.2013.10.011

    View details for Web of Science ID 000332193300013

    View details for PubMedID 24365382

    View details for PubMedCentralID PMC3937533

  • Trainable high resolution melt curve machine learning classifier for large-scale reliable genotyping of sequence variants. PloS one Athamanolap, P. n., Parekh, V. n., Fraley, S. I., Agarwal, V. n., Shin, D. J., Jacobs, M. A., Wang, T. H., Yang, S. n. 2014; 9 (9): e109094


    High resolution melt (HRM) is gaining considerable popularity as a simple and robust method for genotyping sequence variants. However, accurate genotyping of an unknown sample for which a large number of possible variants may exist will require an automated HRM curve identification method capable of comparing unknowns against a large cohort of known sequence variants. Herein, we describe a new method for automated HRM curve classification based on machine learning methods and learned tolerance for reaction condition deviations. We tested this method in silico through multiple cross-validations using curves generated from 9 different simulated experimental conditions to classify 92 known serotypes of Streptococcus pneumoniae and demonstrated over 99% accuracy with 8 training curves per serotype. In vitro verification of the algorithm was tested using sequence variants of a cancer-related gene and demonstrated 100% accuracy with 3 training curves per sequence variant. The machine learning algorithm enabled reliable, scalable, and automated HRM genotyping analysis with broad potential clinical and epidemiological applications.

    View details for DOI 10.1371/journal.pone.0109094

    View details for PubMedID 25275518

    View details for PubMedCentralID PMC4183555

  • Reverse Transcription-PCR-Electrospray Ionization Mass Spectrometry for Rapid Detection of Biothreat and Common Respiratory Pathogens JOURNAL OF CLINICAL MICROBIOLOGY Jeng, K., Hardick, J., Rothman, R., Yang, S., Won, H., Peterson, S., Hsieh, Y., Masek, B. J., Carroll, K. C., Gaydos, C. A. 2013; 51 (10): 3300-3307


    Electrospray ionization mass spectrometry (ESI-MS) analysis of reverse transcription (RT)-PCR amplicons from human respiratory samples allows for broad pathogen identification approximately 8 h after collection. We investigated the performance characteristics of a high-throughput RT-PCR-coupled ESI-MS assay for distinguishing biothreat (BT) agents from common bacterial, fungal, and viral respiratory pathogens in bronchoalveolar lavage (BAL) fluid specimens from subjects with suspected respiratory infections. In a retrospective case series, 202 BAL fluid specimens were collected at the Johns Hopkins Hospital between August 2010 and February 2011 from patients with suspected acute respiratory infections. Samples were processed using standard bacterial, viral, and fungal testing in the clinical microbiology laboratory as part of routine care and then were blindly spiked with either water or nucleic acids from BT organisms (Bacillus anthracis, Yersinia pestis, Francisella tularensis, Brucella spp., Burkholderia spp., and Rickettsia prowazekii) and tested by RT-PCR-ESI-MS. The sensitivities and specificities of RT-PCR-ESI-MS versus standard clinical methods were as follows: for mock BT DNA, 98.5% sensitivity (95% confidence interval [CI], 94.2 to 99.7%) and 100% specificity (95% CI, 93.1 to 100.0%); for bacterial pathogens, 81.8% sensitivity (95% CI, 74.3 to 87.6%) and 73.6% specificity (95% CI, 64.2 to 81.4%); for viral pathogens, 93.3% sensitivity (95% CI, 66.0 to 99.7%) and 97.3% specificity (95% CI, 89.7 to 99.5%); for fungal pathogens, 42.6% sensitivity (95% CI, 29.5 to 56.7%) and 97.8% specificity (95% CI, 91.8 to 99.6%). Our data suggest that RT-PCR-ESI-MS is a useful adjunct to standard culture protocols for rapid detection of both BT and common respiratory pathogens; further study is required for assay validation, especially for fungal detection, and potential implementation.

    View details for DOI 10.1128/JCM.01443-13

    View details for Web of Science ID 000324624300021

    View details for PubMedID 23903543

    View details for PubMedCentralID PMC3811651

  • An all-in-one microfluidic device for parallel DNA extraction and gene analysis (vol 12, pg 1043, 2010) BIOMEDICAL MICRODEVICES Zhang, Y., Park, S., Yang, S., Wang, T. 2013; 15 (2): 383
  • State of virtual reality based disaster preparedness and response training. PLoS currents Hsu, E. B., Li, Y., Bayram, J. D., Levinson, D., Yang, S., Monahan, C. 2013; 5


    The advent of technologically-based approaches to disaster response training through Virtual Reality (VR) environments appears promising in its ability to bridge the gaps of other commonly established training formats. Specifically, the immersive and participatory nature of VR training offers a unique realistic quality that is not generally present in classroom-based or web-based training, yet retains considerable cost advantages over large-scale real-life exercises and other modalities and is gaining increasing acceptance. Currently, numerous government departments and agencies including the U.S. Department of Homeland Security (DHS), the Centers for Disease Control and Prevention (CDC) as well as academic institutions are exploring the unique advantages of VR-based training for disaster preparedness and response. Growing implementation of VR-based training for disaster preparedness and response, conducted either independently or combined with other training formats, is anticipated. This paper reviews several applications of VR-based training in the United States, and reveals advantages as well as potential drawbacks and challenges associated with the implementation of such training platform.

    View details for DOI 10.1371/currents.dis.1ea2b2e71237d5337fa53982a38b2aff

    View details for PubMedID 23653102

    View details for PubMedCentralID PMC3644293

  • Harnessing Genomic Approaches for Infectious Disease Diagnosis in Emergency Medicine: Getting Closer to Prime Time ANNALS OF EMERGENCY MEDICINE Rothman, R. E., Yang, S., Hardick, J., Gaydos, C. A. 2012; 60 (5): 621-623
  • Comparative Analysis of Two Broad-Range PCR Assays for Pathogen Detection in Positive-Blood-Culture Bottles: PCR-High-Resolution Melting Analysis versus PCR-Mass Spectrometry JOURNAL OF CLINICAL MICROBIOLOGY Jeng, K., Gaydos, C. A., Blyn, L. B., Yang, S., Won, H., Matthews, H., Toleno, D., Hsieh, Y., Carroll, K. C., Hardick, J., Masek, B., Kecojevic, A., Sampath, R., Peterson, S., Rothman, R. E. 2012; 50 (10): 3287-3292


    Detection of pathogens in bloodstream infections is important for directing antimicrobial treatment, but current culture-based approaches can be problematic. Broad-range PCR assays which target conserved genomic motifs for postamplification amplicon analysis permit detection of sepsis-causing pathogens. Comparison of different broad-range assays is important for informing future implementation strategies. In this study, we compared positive-blood-culture bottles processed by PCR coupled to high-resolution melting curve analysis (PCR/HRMA) and PCR coupled to electrospray ionization-mass spectrometry (PCR/ESI-MS) to microbiology culture results. Genus-level concordance was 90% (confidence interval [CI], 80 to 96%) for PCR/HRMA and 94% (CI, 85 to 98%) for PCR/ESI-MS. Species-level concordance was 90% (CI, 80 to 96%) for PCR/HRMA and 86% (CI, 75 to 93%) for PCR/ESI-MS. Unlike PCR/HRMA, PCR/ESI-MS was able to resolve polymicrobial samples. Our results demonstrated that the two assays have similar overall concordance rates but may have different roles as potential adjunctive tests with standard blood culture, since each method has different capabilities, advantages, and disadvantages.

    View details for DOI 10.1128/JCM.00677-12

    View details for Web of Science ID 000308870200022

    View details for PubMedID 22855511

    View details for PubMedCentralID PMC3457420

  • A broad range assay for rapid detection and etiologic characterization of bacterial meningitis: performance testing in samples from sub-Sahara DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE Won, H., Yang, S., Gaydos, C., Hardick, J., Ramachandran, P., Hsieh, Y., Kecojevic, A., Njanpop-Lafourcade, B., Mueller, J. E., Tameklo, T. A., Badziklou, K., Gessner, B. D., Rothman, R. E. 2012; 74 (1): 22-27


    This study aimed to conduct a pilot evaluation of broad-based multiprobe polymerase chain reaction (PCR) in clinical cerebrospinal fluid (CSF) samples compared to local conventional PCR/culture methods used for bacterial meningitis surveillance. A previously described PCR consisting of initial broad-based detection of Eubacteriales by a universal probe, followed by Gram typing, and pathogen-specific probes was designed targeting variable regions of the 16S rRNA gene. The diagnostic performance of the 16S rRNA assay in "127 CSF samples was evaluated in samples from patients from Togo, Africa, by comparison to conventional PCR/culture methods. Our probes detected Neisseria meningitidis, Streptococcus pneumoniae, and Haemophilus influenzae. Uniprobe sensitivity and specificity versus conventional PCR were 100% and 54.6%, respectively. Sensitivity and specificity of uniprobe versus culture methods were 96.5% and 52.5%, respectively. Gram-typing probes correctly typed 98.8% (82/83) and pathogen-specific probes identified 96.4% (80/83) of the positives. This broad-based PCR algorithm successfully detected and provided species level information for multiple bacterial meningitis agents in clinical samples.

    View details for DOI 10.1016/j.diagmicrobio.2012.05.015

    View details for Web of Science ID 000308116900005

    View details for PubMedID 22809694

    View details for PubMedCentralID PMC3458235

  • Identification of Bacterial Pathogens in Ascitic Fluids from Patients with Suspected Spontaneous Bacterial Peritonitis by Use of Broad-Range PCR (16S PCR) Coupled with High-Resolution Melt Analysis JOURNAL OF CLINICAL MICROBIOLOGY Hardick, J., Won, H., Jeng, K., Hsieh, Y., Gaydos, C. A., Rothman, R. E., Yang, S. 2012; 50 (7): 2428-2432


    Spontaneous bacterial peritonitis (SBP) can be a severe complication occurring in patients with cirrhosis and ascites, with associated mortality often as high as 40%. Traditional diagnostics for SBP rely on culture techniques for proper diagnosis, although recent reports suggest that the presence of bacterial DNA in peritoneal fluid in patients with cirrhosis and ascites is an indicator of SBP. A previously published broad-range PCR (16S PCR) coupled with high-resolution melt analysis (HRMA) was compared with standard culture techniques for diagnosis of SBP in 106 peritoneal fluid samples from patients with suspected SBP. The sensitivity and specificity for 16S PCR for detecting eubacterial DNA compared with those of standard culture techniques were 100% (17/17) and 91.5% (85/89), respectively. Overall, HRMA concordance with species identification was 70.6% (12/17), although the 5 samples that were discordant at the species level were SBP resulting from a polymicrobial infection, and species-level identification for polymicrobial infections is outside the capability of HRMA. Both the broad-range 16S PCR and HRMA analysis provide useful diagnostic adjunctive assays for clinicians in detecting and identifying pathogens responsible for SBP.

    View details for DOI 10.1128/JCM.00345-12

    View details for Web of Science ID 000307360800040

    View details for PubMedID 22573594

    View details for PubMedCentralID PMC3405590

  • Application of a 16S rRNA PCR-High-Resolution Melt Analysis Assay for Rapid Detection of Salmonella Bacteremia JOURNAL OF CLINICAL MICROBIOLOGY Jeng, K., Yang, S., Won, H., Gaydos, C. A., Hsieh, Y., Kecojevic, A., Carroll, K. C., Hardick, J., Rothman, R. E. 2012; 50 (3): 1122-1124


    Current culture and phenotypic protocols for diagnosing Salmonella infections can be time-consuming. Here, we describe the application of a 16S rRNA PCR coupled to high-resolution melt analysis (HRMA) for species and serotype identification within 6 h of blood sample collection from a patient with Salmonella enterica serotype Enteritidis bacteremia.

    View details for DOI 10.1128/JCM.05121-11

    View details for Web of Science ID 000300997800098

    View details for PubMedID 22205823

    View details for PubMedCentralID PMC3295147

  • Advances in microfluidic PCR for point-of-care infectious disease diagnostics BIOTECHNOLOGY ADVANCES Park, S., Zhang, Y., Lin, S., Wang, T., Yang, S. 2011; 29 (6): 830-839


    Global burdens from existing or emerging infectious diseases emphasize the need for point-of-care (POC) diagnostics to enhance timely recognition and intervention. Molecular approaches based on PCR methods have made significant inroads by improving detection time and accuracy but are still largely hampered by resource-intensive processing in centralized laboratories, thereby precluding their routine bedside- or field-use. Microfluidic technologies have enabled miniaturization of PCR processes onto a chip device with potential benefits including speed, cost, portability, throughput, and automation. In this review, we provide an overview of recent advances in microfluidic PCR technologies and discuss practical issues and perspectives related to implementing them into infectious disease diagnostics.

    View details for DOI 10.1016/j.biotechadv.2011.06.017

    View details for Web of Science ID 000296821900024

    View details for PubMedID 21741465

    View details for PubMedCentralID PMC3186827

  • Rapid Identification of Bacterial Pathogens in Positive Blood Culture Bottles by Use of a Broad-Based PCR Assay Coupled with High-Resolution Melt Analysis (vol 48, pg 3410, 2010) JOURNAL OF CLINICAL MICROBIOLOGY Won, H., Rothman, R., Ramachandran, P., Hsieh, Y., Kecojevic, A., Carroll, K. C., Aird, D., Gaydos, C., Yang, S. 2011; 49 (4): 1705
  • Continuous dielectrophoretic bacterial separation and concentration from physiological media of high conductivity LAB ON A CHIP Park, S., Zhang, Y., Wang, T., Yang, S. 2011; 11 (17): 2893-2900


    Biological sample processing involves purifying target analytes from various sample matrices and concentrating them to a small volume from a large volume of crude sample. This complex process is the major obstacle for developing a microfluidic diagnostic platform. In this study, we present a microfluidic device that can continuously separate and concentrate pathogenic bacterial cells from complex sample matrices such as cerebrospinal fluid and whole blood. Having overcome critical limitations of dielectrophoretic (DEP) operation in physiological media of high conductivity, we utilized target specific DEP techniques to incorporate cell separation, medium exchange, and target concentration into an integrated platform. The proposed microfluidic device can uptake mL volumes of crude biological sample and selectively concentrate target cells into a submicrolitre volume, providing ~10(4) fold of concentration. We designed the device based on the electrokinetic theory and electric field simulation, and tested the device performance with different sample types. The separation efficiency of the device was as high as 97.0% for a bead mixture in TAE buffer and 94.3% and 87.2% for E. coli in human cerebrospinal fluid and blood, respectively. A capture efficiency of 100% was achieved in the concentration chamber. With a relatively simple configuration, the proposed device provides a robust method of continuous sample processing, which can be readily integrated into a fully automated microfluidic diagnostic platform for pathogen detection and quantification.

    View details for DOI 10.1039/c1lc20307j

    View details for Web of Science ID 000293651100012

    View details for PubMedID 21776517

  • A surface topography assisted droplet manipulation platform for biomarker detection and pathogen identification LAB ON A CHIP Zhang, Y., Park, S., Liu, K., Tsuan, J., Yang, S., Wang, T. 2011; 11 (3): 398-406


    This paper reports a droplet microfluidic, sample-to-answer platform for the detection of disease biomarkers and infectious pathogens using crude biosamples. The platform exploited the dual functionality of silica superparamagnetic particles (SSP) for solid phase extraction of DNA and magnetic actuation. This enabled the integration of sample preparation and genetic analysis within discrete droplets, including the steps of cell lysis, DNA binding, washing, elution, amplification and detection. The microfluidic device was self contained, with all reagents stored in droplets, thereby eliminating the need for fluidic coupling to external reagent reservoirs. The device incorporated unique surface topographic features to assist droplet manipulation. Pairs of micro-elevations were created to form slits that facilitated efficient splitting of SSP from droplets. In addition, a compact sample handling stage, which integrated the magnet manipulator, the droplet microfluidic device and a Peltier thermal cycler, was built for convenient droplet manipulation and real-time detection. The feasibility of the platform was demonstrated by analysing ovarian cancer biomarker Rsf-1 and detecting Escherichia coli with real time polymerase chain reaction and real time helicase dependent amplification.

    View details for DOI 10.1039/c0lc00296h

    View details for Web of Science ID 000286326700007

    View details for PubMedID 21046055

  • An all-in-one microfluidic device for parallel DNA extraction and gene analysis BIOMEDICAL MICRODEVICES Zhang, Y., Park, S., Yang, S., Wang, T. 2010; 12 (6): 1043-1049


    We have developed a microfluidic device capable of fully integrated sample preparation and gene analysis from crude biosamples such as whole blood. Our platform takes the advantage of the silica superparamagnetic particle based solid phase extraction to develop an all-in-one scheme that performs cell lysis, DNA binding, washing, elution and the PCR in the same reaction chamber. The device also employs a unique reagent loading scheme, allowing efficient preparation of multiple reactions via a single injection channel. In addition, PCR is performed in a droplet-in-oil manner, eliminating the need for chamber sealing. The combination of these design features greatly reduces the complexity in implementing fully integrated lab-on-a-chip systems for genetic detection, facilitating parallel analysis of multiple samples or genes on a single microchip. The capability of the device is demonstrated by performing DNA isolation from the human whole blood sample and analyzing the Rsf-1 gene using the TaqMan probe based gene specific PCR assays.

    View details for DOI 10.1007/s10544-010-9458-6

    View details for Web of Science ID 000283246500009

    View details for PubMedID 20632111

  • Rapid Identification of Bacterial Pathogens in Positive Blood Culture Bottles by Use of a Broad-Based PCR Assay Coupled with High-Resolution Melt Analysis JOURNAL OF CLINICAL MICROBIOLOGY Won, H., Rothman, R., Ramachandran, P., Hsieh, Y., Kecojevic, A., Carroll, K. C., Aird, D., Gaydos, C., Yang, S. 2010; 48 (9): 3410-3413


    We evaluated a broad-based PCR assay coupled with high-resolution melt analysis for rapid bacterial identification in patients with bacterial sepsis. With a reference library of 60 clinically relevant bacterial species, 52 positive blood culture samples were tested. Our assay identified 46/52 samples at the species level, with 100% concordance to culture findings.

    View details for DOI 10.1128/JCM.00718-10

    View details for Web of Science ID 000281480400068

    View details for PubMedID 20631110

    View details for PubMedCentralID PMC2937718

  • Use of Quantitative Broad-based Polymerase Chain Reaction for Detection and Identification of Common Bacterial Pathogens in Cerebrospinal Fluid ACADEMIC EMERGENCY MEDICINE Rothman, R., Ramachandran, P., Yang, S., Hardick, A., Won, H., Kecojevic, A., Quianzon, C., Hsieh, Y., Gaydos, C. 2010; 17 (7): 741-747


    Conventional laboratory diagnosis of bacterial meningitis based on microscopy followed by culture is time-consuming and has only moderate sensitivity.The objective was to define the limit of detection (LOD), analytic specificity, and performance characteristics of a broad-based quantitative multiprobe polymerase chain reaction (PCR) assay for rapid bacterial detection and simultaneous pathogen-specific identification in patients with suspected meningitis.A PCR algorithm consisting of initial broad-based detection of Eubacteriales by a universal probe, followed by pathogen identification using either pathogen-specific probes or Gram-typing probes, was employed to detect pathogens. The 16S rRNA gene, which contains both conserved and variable regions, was chosen as the target. Pathogen-specific probes were designed for Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Staphylococcus epidermidis, Staphylococcus aureus, Escherichia coli, and Listeria monocytogenes. Gram-positive and -negative typing probes were designed based on conserved regions across all eubacteria. The LOD and time to detection were assessed by dilutional mocked-up samples. A total of 108 convenience cerebrospinal fluid (CSF) clinical samples obtained from the Johns Hopkins Hospital (JHH) microbiology laboratory were tested, and results were compared with hospital microbiologic culture reports.The LOD of the assay ranged from 10(1) to 10(2) colony-forming units (CFU)/mL. Pathogen-specific probes showed no cross-reactivity with other organisms. Time to detection was 3 hours. In clinical specimens, the universal probe correctly detected 16 of 22 culture-positive clinical specimens (sensitivity = 72.7%; 95% confidence interval [CI] = 49.8% to 89.3%), which were all correctly characterized by either pathogen-specific or Gram-typing probes. Adjusted sensitivity after removing probable microbiologic laboratory contaminants was 88.9% (95% CI = 65.3% to 98.6%). The universal probe was negative for 86 of 86 culture-negative specimens.A broad-based multiprobe PCR assay demonstrated strong analytic performance characteristics. Findings from a pilot clinical study showed promise in translation to human subjects, supporting potential utility of the assay as an adjunct to traditional diagnostics for early identification of bacterial meningitis.

    View details for DOI 10.1111/j.1553-2712.2010.00790.x

    View details for Web of Science ID 000279613400017

    View details for PubMedID 20653589

    View details for PubMedCentralID PMC3689214

  • Rapid Identification of Biothreat and Other Clinically Relevant Bacterial Species by Use of Universal PCR Coupled with High-Resolution Melting Analysis JOURNAL OF CLINICAL MICROBIOLOGY Yang, S., Ramachandran, P., Rothman, R., Hsieh, Y., Hardick, A., Won, H., Kecojevic, A., Jackman, J., Gaydos, C. 2009; 47 (7): 2252-2255


    A rapid assay for eubacterial species identification is described using high-resolution melt analysis to characterize PCR products. Unique melt profiles generated from multiple hypervariable regions of the 16S rRNA gene for 100 clinically relevant bacterial pathogens, including category A and B biothreat agents and their surrogates, allowed highly specific species identification.

    View details for DOI 10.1128/JCM.00033-09

    View details for Web of Science ID 000267713000038

    View details for PubMedID 19458181

    View details for PubMedCentralID PMC2708498

  • HIV Seropositivity Predicts Longer Duration of Stay and Rehospitalization Among Nonbacteremic Febrile Injection Drug Users With Skin and Soft Tissue Infections Annual Meeting of the Society-for-Academic-Emergency-Medicine Hsieh, Y., Rothman, R. E., Bartlett, J. G., Yang, S., Kelen, G. D. LIPPINCOTT WILLIAMS & WILKINS. 2008: 398–405


    Skin/soft tissue infections (SSTIs) are the leading cause of hospital admissions among injection drug users (IDUs).We performed a retrospective investigation to determine the epidemiology of SSTIs (ie, cellulitis and/or abscesses) in febrile IDUs, with a focus on bacteriology and potential predictors of increased health care utilization measured by longer length of stay and rehospitalization. Subjects were drawn from a cohort of febrile IDUs presenting to an inner-city emergency department from 1998 to 2004.Of the 295 febrile IDUs with SSTIs, specific discharge diagnoses were cellulitis only (n = 143, 48.5%), abscesses only (n = 113, 38.3%), and both (n = 39, 13.2%). Documented HIV infection rate was 28%. Of note, 10 subjects were newly diagnosed with HIV infection during their visits. Staphylococcus aureus was the leading pathogen, and increasing rates of methicillin-resistant S. aureus emerged over time (before 2001: 4%, 2001-2004: 56%, P < 0.01). HIV seropositivity predicted rehospitalization within 90 days [adjusted hazard ratios and 95% confidence intervals: 2.90 (1.20 to 7.02)]. HIV seropositivity also predicted increased length of stay in those who were nonbacteremic [adjusted hazard ratios and 95% confidence intervals: 1.49 (1.11 to 2.01)].Among febrile IDUs with SSTIs, a strong association between HIV seropositivity and health care resource utilization was found. Accordingly, attention to HIV serostatus should be considered in clinical disposition decisions for this vulnerable high-risk population.

    View details for Web of Science ID 000260844300008

    View details for PubMedID 19186352

  • Rapid polymerase chain reaction-based screening assay for bacterial biothreat agents Annual Meeting of the Society-for-Academic-Emergency-Medicine Yang, S., Rothman, R. E., Hardick, J., Kuroki, M., Hardick, A., Doshi, V., Ramachandran, P., Gaydos, C. A. BLACKWELL PUBLISHING. 2008: 388–92


    To design and evaluate a rapid polymerase chain reaction (PCR)-based assay for detecting Eubacteria and performing early screening for selected Class A biothreat bacterial pathogens.The authors designed a two-step PCR-based algorithm consisting of an initial broad-based universal detection step, followed by specific pathogen identification targeted for identification of the Class A bacterial biothreat agents. A region in the bacterial 16S rRNA gene containing a highly variable sequence flanked by clusters of conserved sequences was chosen as the target for the PCR assay design. A previously described highly conserved region located within the 16S rRNA amplicon was selected as the universal probe (UniProbe, Integrated DNA Technology, Coralville, IA). Pathogen-specific TaqMan probes were designed for Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Performance of the assay was assessed using genomic DNA extracted from the aforementioned biothreat-related organisms (inactivated or surrogate) and other common bacteria.The UniProbe detected the presence of all tested Eubacteria (31/31) with high analytical sensitivity. The biothreat-specific probes accurately identified organisms down to the closely related species and genus level, but were unable to discriminate between very close surrogates, such as Yersinia philomiragia and Bacillus cereus.A simple, two-step PCR-based assay proved capable of both universal bacterial detection and identification of select Class A bacterial biothreat and biothreat-related pathogens. Although this assay requires confirmatory testing for definitive species identification, the method has great potential for use in ED-based settings for rapid diagnosis in cases of suspected Category A bacterial biothreat agents.

    View details for DOI 10.1111/j.1553-2712.2008.00061.x

    View details for Web of Science ID 000254412600014

    View details for PubMedID 18370996

    View details for PubMedCentralID PMC3689204

  • Rapid PCR-based diagnosis of septic arthritis by early gram-type classification and pathogen identification JOURNAL OF CLINICAL MICROBIOLOGY Yang, S., Ramachandran, P., Hardick, A., Hsieh, Y., Quianzon, C., Kuroki, M., Hardick, J., Kecojevic, A., Abeygunawardena, A., Zenilman, J., Melendez, J., Doshi, V., Gaydos, C., Rothman, R. E. 2008; 46 (4): 1386-1390


    Septic arthritis (SA) is a rheumatologic emergency associated with significant morbidity and mortality. Delayed or inadequate treatment of SA can lead to irreversible joint destruction and disability. Current methods of diagnosing SA rely on synovial fluid analysis and culture which are known to be imprecise and time-consuming. We report a novel adaptation of a probe-based real-time PCR assay targeting the 16S rRNA gene for early and accurate diagnosis of bacterial SA. The assay algorithm consists of initial broad-range eubacterial detection, followed by Gram typing and species characterization of the pathogen. The platform demonstrated a high analytical sensitivity with a limit of detection of 10(1) CFU/ml with a panel of SA-related organisms. Gram typing and pathogen-specific probes correctly identified their respective targets in a mock test panel of 36 common clinically relevant pathogens. One hundred twenty-one clinical synovial fluid samples from patients presenting with suspected acute SA were tested. The sensitivity and specificity of the assay were 95% and 97%, respectively, versus synovial fluid culture results. Gram-typing probes correctly identified 100% of eubacterial positive samples as to gram-positive or gram-negative status, and pathogen-specific probes correctly identified the etiologic agent in 16/20 eubacterial positive samples. The total assay time from sample collection to result is 3 h. We have demonstrated that a real-time broad-based PCR assay has high analytical and clinical performance with an improved time to detection versus culture for SA. This assay may be a useful diagnostic adjunct for clinicians, particularly those practicing in the acute care setting where rapid pathogen detection and identification would assist in disposition and treatment decisions.

    View details for DOI 10.1128/JCM.02305-07

    View details for Web of Science ID 000254866400035

    View details for PubMedID 18305128

    View details for PubMedCentralID PMC2292921

  • Global Surveillance of Emerging Influenza Virus Genotypes by Mass Spectrometry PLOS ONE Sampath, R., Russell, K. L., Massire, C., Eshoo, M. W., Harpin, V., Blyn, L. B., Melton, R., Ivy, C., Pennella, T., Li, F., Levene, H., Hall, T. A., Libby, B., Fan, N., Walcott, D. J., Ranken, R., Pear, M., Schink, A., Gutierrez, J., Drader, J., Moore, D., Metzgar, D., Addington, L., Rothman, R., Gaydos, C. A., Yang, S., St George, K., Fuschino, M. E., Dean, A. B., Stallknecht, D. E., Goekjian, G., Yingst, S., Monteville, M., Saad, M. D., Whitehouse, C. A., Baldwin, C., Rudnick, K. H., Hofstadler, S. A., Lemon, S. M., Ecker, D. J. 2007; 2 (5)


    Effective influenza surveillance requires new methods capable of rapid and inexpensive genomic analysis of evolving viral species for pandemic preparedness, to understand the evolution of circulating viral species, and for vaccine strain selection. We have developed one such approach based on previously described broad-range reverse transcription PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology.Analysis of base compositions of RT-PCR amplicons from influenza core gene segments (PB1, PB2, PA, M, NS, NP) are used to provide sub-species identification and infer influenza virus H and N subtypes. Using this approach, we detected and correctly identified 92 mammalian and avian influenza isolates, representing 30 different H and N types, including 29 avian H5N1 isolates. Further, direct analysis of 656 human clinical respiratory specimens collected over a seven-year period (1999-2006) showed correct identification of the viral species and subtypes with >97% sensitivity and specificity. Base composition derived clusters inferred from this analysis showed 100% concordance to previously established clades. Ongoing surveillance of samples from the recent influenza virus seasons (2005-2006) showed evidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were found in approximately 1% of these recent samples providing a view into viral evolution.Thus, rapid RT-PCR/ESI-MS analysis can be used to simultaneously identify all species of influenza viruses with clade-level resolution, identify mixed viral populations and monitor global spread and emergence of novel viral genotypes. This high-throughput method promises to become an integral component of influenza surveillance.

    View details for DOI 10.1371/journal.pone.0000489

    View details for Web of Science ID 000207448800019

    View details for PubMedID 17534439

    View details for PubMedCentralID PMC1876795

  • Communicable respiratory threats in the ED: Tuberculosis, influenza, SARS, and other aerosolized infections EMERGENCY MEDICINE CLINICS OF NORTH AMERICA Rothman, R. E., Hsieh, Y., Yang, S. 2006; 24 (4): 989-?


    Respiratory infections are the most common communicable infectious diseases. EDs are the front line for patients with respiratory infections because of their acute nature and because the ED is the principal site of health care for those at highest risk. These diseases include influenza, tuberculosis, and measles, together accounting for 25% of infectious causes of death worldwide. These are emerging and biothreat agents that follow the same route of transmission, such as pneumonic plague. We discuss epidemiology, pathogenesis, diagnosis, and treatment of each agent. Emphasis is on the ED's role as a public health prevention arena, with attention to education and disease prevention, early identification of disease in patients at risk, and reduction of illnesses.

    View details for DOI 10.1016/j.emc.2006.06.006

    View details for Web of Science ID 000241062500012

    View details for PubMedID 16982349

  • Multiplexed hybridization detection with multicolor colocalization of quantum dot nanoprobes NANO LETTERS Ho, Y. P., Kung, M. C., Yang, S., Wang, T. H. 2005; 5 (9): 1693-1697


    We demonstrate a hybridization detection method using multicolor oligonucleotide-functionalized quantum dots as nanoprobes. In the presence of various target sequences, combinatorial self-assembly of the nanoprobes via independent hybridization reactions leads to the generation of discernible sequence-specific spectral codings. Detection of single-molecule hybridization is achieved by measuring colocalization of individual nanoprobes. Genetic analysis for anthrax pathogenicity through simultaneous detection of multiple relevant sequences is demonstrated using this novel biosensing method as proof-of-concept.

    View details for DOI 10.1021/nl050888v

    View details for Web of Science ID 000231945500011

    View details for PubMedID 16159207

  • Quantitative PCR assay using sputum samples for rapid diagnosis of pneumococcal pneumonia in adult emergency department patients JOURNAL OF CLINICAL MICROBIOLOGY Yang, S., Lin, S., Khalil, A., Gaydos, C., Nuemberger, E., Juan, G., Hardick, J., Bartlett, J. G., Auwaerter, P. G., Rothman, R. E. 2005; 43 (7): 3221-3226


    Accurate diagnosis of pneumococcal pneumonia in the acute-care setting remains a challenge due to the inadequate sensitivity of conventional diagnostic tests. Sputum cultures, which are likely to have the highest diagnostic yields of all specimen types, have been considered unreliable, due to their inability to differentiate colonization from infection. Our objective was to evaluate the potential clinical utility of a rapid quantitative real-time PCR assay using sputum samples for Streptococcus pneumoniae in adult patients with community-acquired pneumonia (CAP). A prospective clinical observational study of consecutively enrolled emergency department patients with CAP was performed; only those patients with excess good-quality sputum samples were included for evaluation. Sputum samples were tested for the presence of S. pneumoniae by using a quantitative PCR that targets the pneumolysin gene. PCR findings were compared with those of a composite reference standard comprising Gram staining of sputum samples and sputum/blood cultures. The area under the curve (AUC) and a log-transformed threshold, which provides the maximal sensitivity and specificity, were calculated. Of 487 subjects enrolled, 129 were evaluable. Receiver operating characteristic curve analysis demonstrated an AUC of 0.87. Sensitivity and specificity were 90.0 percent and 80.0 percent, respectively; positive and negative predictive values were 58.7 percent and 96.2 percent, respectively. We have demonstrated that a quantitative rapid pneumolysin PCR assay has favorable accuracy for diagnosis of pneumococcal pneumonia in adult patients with CAP; this assay may be a useful diagnostic adjunct for clinicians, particularly those practicing in the acute-care setting, where rapid pathogen identification may assist in selection of the most appropriate antibiotics.

    View details for DOI 10.1128/JCM.43.7.3221-3226.2005

    View details for Web of Science ID 000230614900030

    View details for PubMedID 16000439

    View details for PubMedCentralID PMC1169177

  • Real-time PCR for Chlamydia pneumoniae utilizing the Roche lightcycler and a 16S rRNA gene target JOURNAL OF MOLECULAR DIAGNOSTICS Hardick, J., Maldeis, N., Theodore, M., Wood, B. J., Yang, S., Lin, S., Quinn, T., Gaydos, C. 2004; 6 (2): 132-136


    Chlamydia pneumoniae (CPN) causes pneumonia in humans, and has emerged as an important respiratory pathogen. There are also established links between CPN infection and coronary artery disease. Traditional culture methods for CPN detection can be time consuming and difficult. There are a variety of molecular-based amplification methods for CPN detection. These methods are more sensitive than culture, but have the disadvantage of being inconsistent and non-comparable across studies. In this paper, we describe the adaptation of the existing primer set CPN 90/CPN91 for use in a real-time PCR assay using the Roche Lightcycler and a Taqman probe. This assay had an analytical sensitivity of between 4 and 0.4 infection-forming units (IFUs)/PCR reaction. A total of 355 samples were tested for validation of the assay. Tested samples included two standardized panels of blinded samples from culture (N = 70), archived specimens consisting of a CPN dilution series, CPN-spiked porcine aortal tissue and endarterectomy specimens (N = 87). The third group consisted of prospectively collected PBMCs from clinical samples (N = 198). Results were compared to nested PCR, which targets the ompA gene of CPN; TETR PCR, which targets the 16S rRNA gene of CPN; or the known result for the sample. Overall, the assay had a sensitivity of 88.5% (69 of 78) and a specificity of 99.3% (275 of 277). This method should prove useful for accurate, high throughput detection of CPN.

    View details for Web of Science ID 000221002500009

    View details for PubMedID 15096569

    View details for PubMedCentralID PMC1867468

  • Use of the Roche LightCycler instrument in a real-time PCR for Trichomonas vaginalis in urine samples from females and males JOURNAL OF CLINICAL MICROBIOLOGY Hardick, J., Yang, S., Lin, S., Duncan, D., Gaydos, C. 2003; 41 (12): 5619-5622


    Trichomonas vaginalis is the agent of a highly prevalent sexually transmitted infection (STI) that can result in vaginitis, urethritis, and preterm birth. Traditional methods of diagnosis, including wet preparation, can be unreliable. In this study, we describe the adaptation of an existing PCR method for specific detection of T. vaginalis DNA into a rapid real-time PCR assay based on fluorescence resonance energy transfer (FRET) probe chemistry. The FRET-based assay described demonstrated high sensitivity with a detection limit of 1.06 organisms, as well as a high specificity. A total of 253 urine samples collected prospectively from both men and women were tested for T. vaginalis DNA with both the FRET-based assay and a previously validated PCR assay. When the validated PCR assay was used as the "gold standard" and after discrepancies had been resolved, our FRET-based assay demonstrated an analytical sensitivity and specificity of 90.1 and 100%, respectively. Overall results suggest that FRET-based assays can provide rapid, accurate, and high-throughput detection of T. vaginalis and may prove useful in clinical settings and for large-scale screening programs.

    View details for DOI 10.1128/JCM.41.12.5619-5622.2003

    View details for Web of Science ID 000187228800041

    View details for PubMedID 14662951

    View details for PubMedCentralID PMC309023

  • Quantitative multiprobe PCR assay for simultaneous detection and identification to species level of bacterial pathogens JOURNAL OF CLINICAL MICROBIOLOGY Yang, S., Lin, S., Kelen, G. D., Quinn, T. C., Dick, J. D., Gaydos, C. A., Rothman, R. E. 2002; 40 (9): 3449-3454


    We describe a novel adaptation of the TaqMan PCR assay which potentially allows for highly sensitive detection of any eubacterial species with simultaneous species identification. Our system relies on a unique multiprobe design in which a single set of highly conserved sequences encoded by the 16S rRNA gene serves as the primer pair and is used in combination with both an internal highly conserved sequence, the universal probe, and an internal variable region, the species-specific probe. A pre-PCR ultrafiltration step effectively decontaminates or removes background DNA. The TaqMan system described reliabAly detected 14 common bacterial species with a detection limit of 50 fg. Further, highly sensitive and specific pathogen detection was demonstrated with a prototype species-specific probe designed to detect Staphylococcus aureus. This assay has broad potential in the clinical arena for rapid and specific diagnosis of infectious diseases.

    View details for DOI 10.1128/JCM.40.9.3449-3454.2002

    View details for Web of Science ID 000177829900053

    View details for PubMedID 12202592

    View details for PubMedCentralID PMC130696



    Use of transgenic technology in zebrafish has been limited by the inability to efficiently express transgenes in early embryos of F1 and subsequent generations and to rapidly detect transgenic fish. We generated transgenic fish by injecting fertilized eggs with the Escherichia coli lacZ gene under the control of the Xenopus elongation factor 1 alpha transcriptional regulatory element. Four of five lines of transgenic fish we obtained express the lacZ gene in early embryos. The pattern of expression was distinct for each line, with two lines showing extensive expression beginning at approximately the midblastula transition, one showing patchy expression and one showing expression almost exclusively in motor neurons. Expression patterns were stable through the F2 generation in the three lines studied to date. The availability of these lines facilitated the development of a reliable and rapid method for live-staining lacZ-expressing embryos using the substrate fluorescein-di-beta-D-galactopyranoside (FDG). Positive embryos of the two most highly lacZ-expressing lines could be identified after 2-3 min of staining in FDG and then picked out and raised. These observations should prove useful for a variety of studies in zebrafish.

    View details for Web of Science ID A1994MQ97400009

    View details for PubMedID 8293887