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Knoth C, Humphries R, Johnson JK, Patel A, Lima A, Silbert S, Vinjé J. Multicenter evaluation of BioCode GPP for syndromic molecular detection of gastrointestinal pathogens from stool specimens. J Clin Microbiol 2024; 62:e0154523. [PMID: 38329337 PMCID: PMC10935640 DOI: 10.1128/jcm.01545-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Acute gastroenteritis (AGE) is a leading cause of morbidity and mortality worldwide across all age groups that disproportionally affects young children in low- and middle-income countries and immunocompromised patients in high-income countries. Regional outbreaks of AGE are typically detected by traditional microbiological detection methods that target limited organisms and are associated with low sensitivity and lengthy time-to-results. Combined, these may result in repeat testing, imprecise or delayed treatment, and delayed recognition of outbreaks. We conducted a multi-site prospective study comparing the BioCode Gastrointestinal Pathogen Panel (BioCode GPP) for the detection of 17 common bacterial, viral, and protozoan causes of gastroenteritis with reference methods, including stool culture, enzyme immunoassays, pathogen-specific PCR assays, and sequencing. One thousand five hundred fifty-eight residual, de-identified stool samples (unpreserved stool and stool in Cary-Blair transport medium) were enrolled and tested for 11 bacterial, 3 viral, and 3 protozoan pathogens. BioCode GPP and reference methods were positive for 392 (25.2%) and 283 (18.2%) samples, respectively (P < 0.0001). In this study, the BioCode GPP and reference methods detected 69 and 65 specimens positive for Clostridioides difficile, 51 and 48 for enteroaggregative Escherichia coli, 33 and 27 for enterotoxigenic E. coli, 50 and 47 for norovirus GI/GII, and 30 and 22 for rotavirus A, respectively. The BioCode GPP showed good positive and negative agreements for each pathogen ranging from 89.5% to 100%, with overall sensitivity and specificity of 96.1% and 99.7%, post adjudication. The BioCode GPP detected >1 pathogens in 49 samples, representing 12.5% of the total 392 positive specimens. IMPORTANCE This study highlights performance of a novel technology for timely and accurate detection and differentiation of 17 common bacterial, viral, and protozoan causes of gastroenteritis. Utilizing molecular tests such as the BioCode Gastrointestinal Pathogen Panel may improve the detection of gastrointestinal pathogens and provide actionable results, particularly for patient populations at most risk.
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Affiliation(s)
| | - Romney Humphries
- University of California Los Angeles Medical Center, Los Angeles, California, USA
| | - J. Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Anami Patel
- Le Bonheur Children’s Hospital, Memphis, Tennessee, USA
| | | | | | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Zhang X, Knoth C, Pham A, Lima A, Dominguez R, Ibarra-Flores I, Lopez JC, Uy D, Silbert S, Patel A, Aye M, Tang YW, Dien Bard J. The Clinical Performance of the BioCode Respiratory Pathogen Panel for the Detection of Viruses and Bacteria from Nasopharyngeal Swabs. Microbiol Spectr 2023; 11:e0404422. [PMID: 37039708 PMCID: PMC10269715 DOI: 10.1128/spectrum.04044-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/12/2023] Open
Abstract
Early detection of microbial pathogens causing respiratory tract infection plays a crucial role in clinical management. The BioCode Respiratory Pathogen Panel (BioCode RPP) utilizes reverse transcriptase PCR (RT-PCR) in combination with barcoded magnetic beads to amplify, detect, and identify respiratory pathogens. This panel qualitatively detects and identifies 14 viruses, including influenza virus A with H1 pdm09, H1, and H3 subtyping; influenza B; respiratory syncytial virus (RSV); human metapneumovirus; parainfluenza virus 1; parainfluenza virus 2; parainfluenza virus 3; parainfluenza virus 4; coronavirus (229E, NL63, OC43, and HKU1); adenovirus; and human rhinovirus/enterovirus, and 3 bacteria, including Chlamydia pneumoniae, Mycoplasma pneumoniae, and Bordetella pertussis. Reproducibility, which was assessed with contrived specimens containing 12 targets at 3 clinical sites, with 2 operators at each site for 5 days, was 99.4% for Flu A H3 and Flu B, 98.9% for RSV, and 100% for the remaining 9 targets assayed. A multicenter clinical trial evaluated the performance of the BioCode RPP with 2,647 nasopharyngeal swab specimens from 5 geographically distinct sites and revealed comparable performance between the BioCode RPP and FilmArray Respiratory Panel (FA-RP). Specifically, the positive percent agreements (PPAs) for various pathogens ranged between 80.8% and 100% compared with the FA-RP (1.7 and 2.0). Negative percent agreement ranged from 98.4% to 100% for BioCode RPP. The BioCode RPP also offers scalable automated testing capability of up to 96 specimens in a single run with total sample-to-result time under 5 h. The invalid rate of the BioCode RPP on initial testing was 1.0% (26/2,649). IMPORTANCE Early detection of microbial pathogens causing respiratory tract infection plays a crucial role in clinical management. The BioCode Respiratory Pathogen Panel (BioCode RPP) is a high-throughput test that utilizes RT-PCR in combination with barcoded magnetic beads to amplify, detect, and identify 17 respiratory pathogens, including 14 viruses and 3 bacteria. This study summarizes data generated from a multicenter clinical trial evaluating the performance of the BioCode RPP on 2,647 nasopharyngeal swab specimens from five geographically distinct sites.
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Affiliation(s)
- Xin Zhang
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Sichuan Academy of Medicine & Sichuan Provincial People’s Hospital, Chengdu, China
| | - Colleen Knoth
- Applied BioCode Inc., Santa Fe Springs, California, USA
| | - Anh Pham
- Applied BioCode Inc., Santa Fe Springs, California, USA
| | | | - Rosario Dominguez
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Irvin Ibarra-Flores
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Juan C. Lopez
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dominic Uy
- Tampa General Hospital, Tampa, Florida, USA
| | | | | | - Michael Aye
- Applied BioCode Inc., Santa Fe Springs, California, USA
| | - Yi-Wei Tang
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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Rodriguez-Salus M, Bektas Y, Schroeder M, Knoth C, Vu T, Roberts P, Kaloshian I, Eulgem T. The Synthetic Elicitor 2-(5-Bromo-2-Hydroxy-Phenyl)-Thiazolidine-4-Carboxylic Acid Links Plant Immunity to Hormesis. Plant Physiol 2016; 170:444-58. [PMID: 26530314 PMCID: PMC4704575 DOI: 10.1104/pp.15.01058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/28/2015] [Indexed: 05/03/2023]
Abstract
Synthetic elicitors are drug-like compounds that induce plant immune responses but are structurally distinct from natural defense elicitors. Using high-throughput screening, we previously identified 114 synthetic elicitors that activate the expression of a pathogen-responsive reporter gene in Arabidopsis (Arabidopsis thaliana). Here, we report on the characterization of one of these compounds, 2-(5-bromo-2-hydroxy-phenyl)-thiazolidine-4-carboxylic acid (BHTC). BHTC induces disease resistance of plants against bacterial, oomycete, and fungal pathogens and has a unique mode of action and structure. Surprisingly, we found that low doses of BHTC enhanced root growth in Arabidopsis, while high doses of this compound inhibited root growth, besides inducing defense. These effects are reminiscent of the hormetic response, which is characterized by low-dose stimulatory effects of a wide range of agents that are toxic or inhibitory at higher doses. Like its effects on defense, BHTC-induced hormesis in Arabidopsis roots is partially dependent on the WRKY70 transcription factor. Interestingly, BHTC-induced root hormesis is also affected in the auxin-response mutants axr1-3 and slr-1. By messenger RNA sequencing, we uncovered a dramatic difference between transcriptional profiles triggered by low and high doses of BHTC. Only high levels of BHTC induce typical defense-related transcriptional changes. Instead, low BHTC levels trigger a coordinated intercompartmental transcriptional response manifested in the suppression of photosynthesis- and respiration-related genes in the nucleus, chloroplasts, and mitochondria as well as the induction of development-related nuclear genes. Taken together, our functional characterization of BHTC links defense regulation to hormesis and provides a hypothetical transcriptional scenario for the induction of hormetic root growth.
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Affiliation(s)
- Melinda Rodriguez-Salus
- ChemGen Integrative Graduate Education and Research Traineeship Program (M.R.-S., M.S., C.K., T.E.), Center for Plant Cell Biology, Institute for Integrative Genome Biology (M.R.-S., Y.B., M.S., C.K., I.K., T.E.), Department of Botany and Plant Sciences (M.R.-S., Y.B., M.S., C.K., T.V., T.E.), and Department of Nematology (P.R., I.K.), University of California, Riverside, California 92521
| | - Yasemin Bektas
- ChemGen Integrative Graduate Education and Research Traineeship Program (M.R.-S., M.S., C.K., T.E.), Center for Plant Cell Biology, Institute for Integrative Genome Biology (M.R.-S., Y.B., M.S., C.K., I.K., T.E.), Department of Botany and Plant Sciences (M.R.-S., Y.B., M.S., C.K., T.V., T.E.), and Department of Nematology (P.R., I.K.), University of California, Riverside, California 92521
| | - Mercedes Schroeder
- ChemGen Integrative Graduate Education and Research Traineeship Program (M.R.-S., M.S., C.K., T.E.), Center for Plant Cell Biology, Institute for Integrative Genome Biology (M.R.-S., Y.B., M.S., C.K., I.K., T.E.), Department of Botany and Plant Sciences (M.R.-S., Y.B., M.S., C.K., T.V., T.E.), and Department of Nematology (P.R., I.K.), University of California, Riverside, California 92521
| | - Colleen Knoth
- ChemGen Integrative Graduate Education and Research Traineeship Program (M.R.-S., M.S., C.K., T.E.), Center for Plant Cell Biology, Institute for Integrative Genome Biology (M.R.-S., Y.B., M.S., C.K., I.K., T.E.), Department of Botany and Plant Sciences (M.R.-S., Y.B., M.S., C.K., T.V., T.E.), and Department of Nematology (P.R., I.K.), University of California, Riverside, California 92521
| | - Trang Vu
- ChemGen Integrative Graduate Education and Research Traineeship Program (M.R.-S., M.S., C.K., T.E.), Center for Plant Cell Biology, Institute for Integrative Genome Biology (M.R.-S., Y.B., M.S., C.K., I.K., T.E.), Department of Botany and Plant Sciences (M.R.-S., Y.B., M.S., C.K., T.V., T.E.), and Department of Nematology (P.R., I.K.), University of California, Riverside, California 92521
| | - Philip Roberts
- ChemGen Integrative Graduate Education and Research Traineeship Program (M.R.-S., M.S., C.K., T.E.), Center for Plant Cell Biology, Institute for Integrative Genome Biology (M.R.-S., Y.B., M.S., C.K., I.K., T.E.), Department of Botany and Plant Sciences (M.R.-S., Y.B., M.S., C.K., T.V., T.E.), and Department of Nematology (P.R., I.K.), University of California, Riverside, California 92521
| | - Isgouhi Kaloshian
- ChemGen Integrative Graduate Education and Research Traineeship Program (M.R.-S., M.S., C.K., T.E.), Center for Plant Cell Biology, Institute for Integrative Genome Biology (M.R.-S., Y.B., M.S., C.K., I.K., T.E.), Department of Botany and Plant Sciences (M.R.-S., Y.B., M.S., C.K., T.V., T.E.), and Department of Nematology (P.R., I.K.), University of California, Riverside, California 92521
| | - Thomas Eulgem
- ChemGen Integrative Graduate Education and Research Traineeship Program (M.R.-S., M.S., C.K., T.E.), Center for Plant Cell Biology, Institute for Integrative Genome Biology (M.R.-S., Y.B., M.S., C.K., I.K., T.E.), Department of Botany and Plant Sciences (M.R.-S., Y.B., M.S., C.K., T.V., T.E.), and Department of Nematology (P.R., I.K.), University of California, Riverside, California 92521
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Knoth C, Salus MS, Girke T, Eulgem T. The synthetic elicitor 3,5-dichloroanthranilic acid induces NPR1-dependent and NPR1-independent mechanisms of disease resistance in Arabidopsis. Plant Physiol 2009; 150:333-47. [PMID: 19304930 PMCID: PMC2675713 DOI: 10.1104/pp.108.133678] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 03/17/2009] [Indexed: 05/20/2023]
Abstract
Immune responses of Arabidopsis (Arabidopsis thaliana) are at least partially mediated by coordinated transcriptional up-regulation of plant defense genes, such as the Late/sustained Up-regulation in Response to Hyaloperonospora parasitica (LURP) cluster. We found a defined region in the promoter of the LURP member CaBP22 to be important for this response. Using a CaBP22 promoter-reporter fusion, we have established a robust and specific high-throughput screening system for synthetic defense elicitors that can be used to trigger defined subsets of plant immune responses. Screening a collection of 42,000 diversity-oriented molecules, we identified 114 candidate LURP inducers. One representative, 3,5-dichloroanthranilic acid (DCA), efficiently induced defense reactions to the phytopathogens H. parasitica and Pseudomonas syringae. In contrast to known salicylic acid analogs, such as 2,6-dichloroisonicotinic acid (INA), which exhibit a long-lasting defense-inducing activity and are fully dependent on the transcriptional cofactor NPR1 (for Nonexpresser of Pathogenesis-Related genes1), DCA acts transiently and is only partially dependent on NPR1. Microarray analyses revealed a cluster of 142 DCA- and INA-responsive genes that show a pattern of differential expression coinciding with the kinetics of DCA-mediated disease resistance. These ACID genes (for Associated with Chemically Induced Defense) constitute a core gene set associated with chemically induced disease resistance, many of which appear to encode components of the natural immune system of Arabidopsis.
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Affiliation(s)
- Colleen Knoth
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, Department of Botany and Plant Sciences, University of California at Riverside, Riverside, California 92521, USA
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