1
|
Damhorst GL, Lin J, Frediani JK, Sullivan JA, Westbrook A, McLendon K, Baugh TJ, O'Sick WH, Roback JD, Piantadosi AL, Waggoner JJ, Bassit L, Rao A, Greenleaf M, O'Neal JW, Swanson S, Pollock NR, Martin GS, Lam WA, Levy JM. Comparison of RT-PCR and antigen test sensitivity across nasopharyngeal, nares, and oropharyngeal swab, and saliva sample types during the SARS-CoV-2 omicron variant. Heliyon 2024; 10:e27188. [PMID: 38500996 PMCID: PMC10945130 DOI: 10.1016/j.heliyon.2024.e27188] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 11/29/2023] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Limited data highlight the need to understand differences in SARS-CoV-2 omicron (B.1.1.529) variant viral load between the gold standard nasopharyngeal (NP) swab, mid-turbinate (MT)/anterior nasal swabs, oropharyngeal (OP) swabs, and saliva. MT, OP, and saliva samples from symptomatic individuals in Atlanta, GA, in January 2022 and longitudinal samples from a small familial cohort were tested by both RT-PCR and ultrasensitive antigen assays. Higher concentrations in the nares were observed in the familial cohort, but a dominant sample type was not found among 39 cases in the cross-sectional cohort. The composite of positive MT or OP assay for both RT-PCR and antigen assay trended toward higher diagnostic yield but did not achieve significant difference. Our data did not identify a singular preferred sample type for SARS-CoV-2 testing, but higher levels of saliva nucleocapsid, a trend toward higher yield of composite OP/MT result, and association of apparent MT or OP predominance with symptoms warrant further study.
Collapse
Affiliation(s)
- Gregory L. Damhorst
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Division of Infectious Diseases, Emory University School of Medicine, USA
| | - Jessica Lin
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, USA
| | - Jennifer K. Frediani
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Nell Hodgson Woodruff School of Nursing, Emory University, USA
| | - Julie A. Sullivan
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Department of Pediatrics, Emory University School of Medicine, USA
| | - Adrianna Westbrook
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University School of Medicine, USA
| | - Kaleb McLendon
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, USA
| | - Tyler J. Baugh
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, USA
| | - William H. O'Sick
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, USA
| | - John D. Roback
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, USA
| | - Anne L. Piantadosi
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Division of Infectious Diseases, Emory University School of Medicine, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, USA
| | - Jesse J. Waggoner
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Division of Infectious Diseases, Emory University School of Medicine, USA
| | - Leda Bassit
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, USA
| | - Anuradha Rao
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Department of Pediatrics, Emory University School of Medicine, USA
| | - Morgan Greenleaf
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
| | - Jared W. O'Neal
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Emory University School of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, USA
| | - Seegar Swanson
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
| | - Nira R. Pollock
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Department of Laboratory Medicine, Boston Children's Hospital, USA
| | - Greg S. Martin
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Emory University School of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, USA
| | - Wilbur A. Lam
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, USA
- Department of Pediatrics, Emory University School of Medicine, USA
- Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, USA
| | - Joshua M. Levy
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA
- Emory University School of Medicine, Department of Otolaryngology-Head and Neck Surgery, USA
- Sinonasal and Olfaction Program, National Institute on Deafness and Other Communication Disorders, NIDCD/NIH
| |
Collapse
|
2
|
Frediani JK, Parsons R, McLendon KB, Westbrook AL, Lam W, Martin G, Pollock NR. The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs. Clin Infect Dis 2024; 78:301-307. [PMID: 37768707 PMCID: PMC10874267 DOI: 10.1093/cid/ciad582] [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: 05/17/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Early in the coronavirus disease 2019 (COVID-19) pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. METHODS We assessed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A viral loads relative to symptom duration in symptomatic adults (≥16 years) presenting for testing in Georgia (4/2022-4/2023; Omicron variant predominant). Participants provided symptom duration and recent testing history. Nasal swabs were tested by Xpert Xpress SARS-CoV-2/Flu/RSV assay and cycle threshold (Ct) values recorded. Nucleoprotein concentrations in SARS-CoV-2 polymerase chain reaction (PCR)-positive samples were measured by single molecule array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. RESULTS Of 348 newly-diagnosed SARS-CoV-2 PCR-positive individuals (65.5% women, median 39.2 years), 317/348 (91.1%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth/fifth day. Ag RDT sensitivity estimates were 30.0%-60.0% on the first day, 59.2%-74.8% on the third day, and 80.0%-93.3% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0 years), median influenza viral loads peaked on the second day of symptoms. CONCLUSIONS In a highly immune adult population, median SARS-CoV-2 viral loads peaked around the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza.
Collapse
Affiliation(s)
- Jennifer K Frediani
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Richard Parsons
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Kaleb B McLendon
- Emory/Children's Laboratory for Innovative Assay Development, Department of Pathology, Emory University, Atlanta, Georgia, USA
| | - Adrianna L Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Greg Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
3
|
Katzenschlager S, Brümmer LE, Schmitz S, Tolle H, Manten K, Gaeddert M, Erdmann C, Lindner A, Tobian F, Grilli M, Pollock NR, Macé A, Erkosar B, Carmona S, Ongarello S, Johnson CC, Sacks JA, Denkinger CM, Yerlikaya S. Comparing SARS-CoV-2 antigen-detection rapid diagnostic tests for COVID-19 self-testing/self-sampling with molecular and professional-use tests: a systematic review and meta-analysis. Sci Rep 2023; 13:21913. [PMID: 38081881 PMCID: PMC10713601 DOI: 10.1038/s41598-023-48892-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Self-testing is an effective tool to bridge the testing gap for several infectious diseases; however, its performance in detecting SARS-CoV-2 using antigen-detection rapid diagnostic tests (Ag-RDTs) has not been systematically reviewed. This study aimed to inform WHO guidelines by evaluating the accuracy of COVID-19 self-testing and self-sampling coupled with professional Ag-RDT conduct and interpretation. Articles on this topic were searched until November 7th, 2022. Concordance between self-testing/self-sampling and fully professional-use Ag-RDTs was assessed using Cohen's kappa. Bivariate meta-analysis yielded pooled performance estimates. Quality and certainty of evidence were evaluated using QUADAS-2 and GRADE tools. Among 43 studies included, twelve reported on self-testing, and 31 assessed self-sampling only. Around 49.6% showed low risk of bias. Overall concordance with professional-use Ag-RDTs was high (kappa 0.91 [95% confidence interval (CI) 0.88-0.94]). Comparing self-testing/self-sampling to molecular testing, the pooled sensitivity and specificity were 70.5% (95% CI 64.3-76.0) and 99.4% (95% CI 99.1-99.6), respectively. Higher sensitivity (i.e., 93.6% [95% CI 90.4-96.8] for Ct < 25) was estimated in subgroups with higher viral loads using Ct values as a proxy. Despite high heterogeneity among studies, COVID-19 self-testing/self-sampling exhibits high concordance with professional-use Ag-RDTs. This suggests that self-testing/self-sampling can be offered as part of COVID-19 testing strategies.Trial registration: PROSPERO: CRD42021250706.
Collapse
Affiliation(s)
- Stephan Katzenschlager
- Department of Anesthesiology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Lukas E Brümmer
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
- German Center for Infection Research (DZIF), Partner Site Heidelberg University Hospital, Heidelberg, Germany
| | - Stephani Schmitz
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hannah Tolle
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Katharina Manten
- Department of Anesthesiology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Mary Gaeddert
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | | | - Andreas Lindner
- Charité Center for Global Health, Institute of International Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frank Tobian
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | | | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | | | | | | | - Cheryl C Johnson
- Global HIV, Hepatitis and STIs Programmes, World Health Organization, Geneva, Switzerland
| | - Jilian A Sacks
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Claudia M Denkinger
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
- German Center for Infection Research (DZIF), Partner Site Heidelberg University Hospital, Heidelberg, Germany
| | - Seda Yerlikaya
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
| |
Collapse
|
4
|
Rao A, Westbrook A, Bassit L, Parsons R, Fitts E, Greenleaf M, McLendon K, Sullivan JA, O’Sick W, Baugh T, Bowers HB, Frank F, Wang E, Le M, Frediani J, Roychoudhury P, Greninger AL, Jerris R, Pollock NR, Ortlund EA, Roback JD, Lam WA, Piantadosi A. Sensitivity of rapid antigen tests against SARS-CoV-2 Omicron and Delta variants. J Clin Microbiol 2023; 61:e0013823. [PMID: 37728336 PMCID: PMC10654096 DOI: 10.1128/jcm.00138-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/22/2023] [Indexed: 09/21/2023] Open
Abstract
Rapid antigen tests (RATs) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of 10 commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using both individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR cycle threshold (CT) value (a rough proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using C T value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.
Collapse
Affiliation(s)
- Anuradha Rao
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Adrianna Westbrook
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Leda Bassit
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia, USA
| | - Richard Parsons
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Eric Fitts
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Morgan Greenleaf
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kaleb McLendon
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Julie A. Sullivan
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - William O’Sick
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Tyler Baugh
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Heather B. Bowers
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ethan Wang
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mimi Le
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jennifer Frediani
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | | | - Robert Jerris
- Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eric A. Ortlund
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John D. Roback
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Wilbur A. Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center at Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| |
Collapse
|
5
|
Nelson SB, Brenner IR, Homan E, Lee SB, Bongiorno C, Pollock NR, Ciaranello A. Evaluation of "Test to Return" after COVID-19 Diagnosis in a Massachusetts Public School District. J Sch Health 2023; 93:877-882. [PMID: 37272202 DOI: 10.1111/josh.13357] [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] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/12/2022] [Accepted: 05/21/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Per Centers for Disease Control and Prevention guidance, students with COVID-19 may end isolation after 5 days if symptoms are improving; some individuals may still be contagious. Rapid antigen testing identifies possibly infectious virus. We report on a test-to-return (TTR) program in a Massachusetts school district to inform policy decisions about return to school after COVID-19. METHODS During the 2021-2022 Omicron BA.1 surge, students with COVID-19 could return on day 6-10 if they met symptom criteria and had a negative rapid test; students with positive rapid tests and those who declined TTR remained isolated until day 11. TTR positivity rates were compared by grade level, vaccination status, symptom status, and day of infection. RESULTS 31.4% of students had a positive TTR rapid test; there were no differences by grade or vaccination status. Ever-symptomatic students were more likely to have a positive rapid test (75/174 [43.1%] vs 18/104 [17.3%]). For ever-symptomatic students, TTR positivity decreased by day of infection. CONCLUSIONS A substantial proportion of students may still be contagious 6 days after onset of COVID-19 infection. TTR programs may increase or reduce missed school days, depending on when return is otherwise allowed (day 6 or 11). The impact of TTR programs on school-associated transmission remains unknown.
Collapse
Affiliation(s)
- Sandra B Nelson
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Isaac Ravi Brenner
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA
| | | | | | | | - Nira R Pollock
- Harvard Medical School, Boston, MA; Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA
| | - Andrea Ciaranello
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA; Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA
| |
Collapse
|
6
|
Sandora TJ, Kociolek LK, Williams DN, Daugherty K, Geer C, Cuddemi C, Chen X, Xu H, Savage TJ, Banz A, Garey KW, Gonzales-Luna AJ, Kelly CP, Pollock NR. Baseline stool toxin concentration is associated with risk of recurrence in children with Clostridioides difficile infection. Infect Control Hosp Epidemiol 2023; 44:1403-1409. [PMID: 36624698 PMCID: PMC10330943 DOI: 10.1017/ice.2022.310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND In adults with Clostridioides difficile infection (CDI), higher stool concentrations of toxins A and B are associated with severe baseline disease, CDI-attributable severe outcomes, and recurrence. We evaluated whether toxin concentration predicts these presentations in children with CDI. METHODS We conducted a prospective cohort study of inpatients aged 2-17 years with CDI who received treatment. Patients were followed for 40 days after diagnosis for severe outcomes (intensive care unit admission, colectomy, or death, categorized as CDI primarily attributable, CDI contributed, or CDI not contributing) and recurrence. Baseline stool toxin A and B concentrations were measured using ultrasensitive single-molecule array assay, and 12 plasma cytokines were measured when blood was available. RESULTS We enrolled 187 pediatric patients (median age, 9.6 years). Patients with severe baseline disease by IDSA-SHEA criteria (n = 34) had nonsignificantly higher median stool toxin A+B concentration than those without severe disease (n = 122; 3,217.2 vs 473.3 pg/mL; P = .08). Median toxin A+B concentration was nonsignificantly higher in children with a primarily attributed severe outcome (n = 4) versus no severe outcome (n = 148; 19,472.6 vs 429.1 pg/mL; P = .301). Recurrence occurred in 17 (9.4%) of 180 patients. Baseline toxin A+B concentration was significantly higher in patients with versus without recurrence: 4,398.8 versus 280.8 pg/mL (P = .024). Plasma granulocyte colony-stimulating factor concentration was significantly higher in CDI patients versus non-CDI diarrhea controls: 165.5 versus 28.5 pg/mL (P < .001). CONCLUSIONS Higher baseline stool toxin concentrations are present in children with CDI recurrence. Toxin quantification should be included in CDI treatment trials to evaluate its use in severity assessment and outcome prediction.
Collapse
Affiliation(s)
- Thomas J. Sandora
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Larry K. Kociolek
- Division of Infectious Diseases, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - David N. Williams
- Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology (K.D., C.G., C.C., C.K) and Division of Infectious Diseases (N.R.P.), Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Christine Geer
- Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, MA, 02115, USA
- Division of Gastroenterology (K.D., C.G., C.C., C.K) and Division of Infectious Diseases (N.R.P.), Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Christine Cuddemi
- Division of Gastroenterology (K.D., C.G., C.C., C.K) and Division of Infectious Diseases (N.R.P.), Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Xinhua Chen
- Division of Gastroenterology (K.D., C.G., C.C., C.K) and Division of Infectious Diseases (N.R.P.), Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Hua Xu
- Division of Gastroenterology (K.D., C.G., C.C., C.K) and Division of Infectious Diseases (N.R.P.), Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Timothy J. Savage
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02120, USA
| | - Alice Banz
- bioMerieux, Marcy L’Etoile, 69280, France
| | - Kevin W. Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, 77204, USA
| | - Anne J. Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, 77204, USA
| | - Ciarán P. Kelly
- Division of Gastroenterology (K.D., C.G., C.C., C.K) and Division of Infectious Diseases (N.R.P.), Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Nira R. Pollock
- Division of Gastroenterology (K.D., C.G., C.C., C.K) and Division of Infectious Diseases (N.R.P.), Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
- Department of Laboratory Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
| |
Collapse
|
7
|
Nelson SB, Dugdale CM, Brenner IR, Crawford A, Bilinski A, Cosar D, Pollock NR, Ciaranello A. Prevalence and Risk Factors for School-Associated Transmission of SARS-CoV-2. JAMA Health Forum 2023; 4:e232310. [PMID: 37540523 PMCID: PMC10403780 DOI: 10.1001/jamahealthforum.2023.2310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/30/2023] [Indexed: 08/05/2023] Open
Abstract
Importance School-associated SARS-CoV-2 transmission is described as uncommon, although the true transmission rate is unknown. Objective To identify the SARS-CoV-2 secondary attack rate (SAR) in schools and factors associated with transmission. Design, Setting, and Participants This cohort study examined the risk of school-based transmission of SARS-CoV-2 among kindergarten through grade 12 students and staff in 10 Massachusetts school districts during 2 periods: fall 2020/spring 2021 (F20/S21) and fall 2021 (F21). School staff collected data on SARS-CoV-2 index cases and school-based contacts, and SAR was defined as the proportion of contacts acquiring SARS-CoV-2 infection. Exposure SARS-CoV-2. Main Outcomes and Measures Potential factors associated with transmission, including grade level, masking, exposure location, vaccination history, and Social Vulnerability Index (SVI), were analyzed using univariable and multivariable logistic regression models. Results For F20/S21, 8 school districts (70 schools, >33 000 students) were included and reported 435 index cases (151 staff, 216 students, and 68 missing role) with 1771 school-based contacts (278 staff, 1492 students, and 1 missing role). For F21, 5 districts (34 schools, >18 000 students) participated and reported 309 index cases (37 staff, 207 students, and 65 missing role) with 1673 school-based contacts (107 staff and 1566 students). The F20/S21 SAR was 2.2% (lower bound, 1.6%; upper bound, 26.7%), and the F21 SAR was 2.8% (lower bound, 2.6%; upper bound, 7.4%). In multivariable analysis, during F20/S21, masking was associated with a lower odds of transmission compared with not masking (odds radio [OR], 0.12; 95% CI, 0.04-0.40; P < .001). In F21, classroom exposure vs out-of-classroom exposure was associated with increased odds of transmission (OR, 2.47; 95% CI, 1.07-5.66; P = .02); a fully vaccinated vs unvaccinated contact was associated with a lower odds of transmission (OR, 0.04; 95% CI, 0.00-0.62; P < .001). In both periods, a higher SVI was associated with a greater odds of transmission. Conclusions and Relevance In this study of Massachusetts schools, the SAR for SARS-CoV-2 among school-based contacts was low during 2 periods, and factors associated with transmission risk varied over time. These findings suggest that ongoing surveillance efforts may be essential to ensure that both targeted resources and mitigation practices remain optimal and relevant for disease prevention.
Collapse
Affiliation(s)
- Sandra B. Nelson
- Division of Infectious Diseases, Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, Massachusetts
| | - Caitlin M. Dugdale
- Division of Infectious Diseases, Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, Massachusetts
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston
| | - Isaac Ravi Brenner
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston
| | - Allison Crawford
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston
| | - Alyssa Bilinski
- Department of Health Services, Policy and Practice and Department of Biostatistics, Brown School of Public Health, Providence, Rhode Island
| | - Duru Cosar
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston
| | - Nira R. Pollock
- Harvard Medical School, Boston, Massachusetts
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts
| | - Andrea Ciaranello
- Division of Infectious Diseases, Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, Massachusetts
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston
| |
Collapse
|
8
|
Mesman AW, Calderon RI, Hauns L, Pollock NR, Mendoza M, Holmberg RC, Franke MF. Detection of Mycobacterium tuberculosis transrenal DNA in urine samples among adult patients in Peru. medRxiv 2023:2023.07.26.23293199. [PMID: 37546779 PMCID: PMC10402216 DOI: 10.1101/2023.07.26.23293199] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Diagnosis of tuberculosis (TB) relies on a sputum sample, which cannot be obtained from all symptomatic patients. Mycobacterium tuberculosis (Mtb) transrenal DNA (trDNA) has been detected in urine, an easily obtainable, noninvasive, alternative sample type. However, reported sensitivities have been variable and likely depend on collection/assay procedures and aspects of trDNA biology. We analyzed three serial urine samples from each of 75 adults with culture-confirmed pulmonary TB disease in Lima, Peru for detection of trDNA using short-fragment real-time PCR. Additionally, we examined host, urine, and sampling factors associated with detection. Overall sample sensitivity was 38% (95% Confidence Interval [CI] 30-45%). On a patient level (i.e., any of three samples positive), sensitivity was 73% (95% CI: 62-83%). Sensitivity was highest among samples from patients with smear-positive TB, 92% (95% CI: 62-100%). Specificity from a single sample from each of 10 healthy controls was 100% (95% CI: 69-100%). Adjusting our assay positivity threshold increased patient-level sensitivity to 88% (95% CI: 78-94%) overall without affecting the specificity. We did not find associations between Mtb trDNA detection and either patient characteristics or urine sample characteristics. Overall, our results support the potential of trDNA detection for TB diagnosis.
Collapse
Affiliation(s)
- Annelies W Mesman
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA
| | | | | | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA
| | | | | | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA
| |
Collapse
|
9
|
Frediani JK, Parsons R, McLendon KB, Westbrook AL, Lam W, Martin G, Pollock NR. The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs. medRxiv 2023:2023.05.09.23289735. [PMID: 37214887 PMCID: PMC10197800 DOI: 10.1101/2023.05.09.23289735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Early in the COVID-19 pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. Methods We assessed SARS-CoV-2 and influenza A viral loads relative to symptom duration in recently-tested adults. Symptomatic participants ≥16y presenting to testing sites in Georgia (4/2022-4/2023; Omicron variant predominant) provided symptom duration. Nasal swab samples were tested by the Xpert Xpress SARS-CoV-2/Flu/RSV assay and Ct values recorded. Nucleoprotein concentrations in SARS-CoV-2 PCR-positive samples were measured by Single Molecule Array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. Results Of 621 SARS-CoV-2 PCR-positive individuals (64.1% women, median 40.9y), 556/621 (89.5%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth day. Ag RDT sensitivity estimates were 35.7-71.4% on the first day, 63.9-78.7% on the third day, and 78.6-90.6% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0y), median influenza viral loads peaked on the second day of symptoms. Conclusions In a highly immune adult population, median SARS-CoV-2 viral loads peaked on the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza. Key Points In a highly immune adult population, median SARS-CoV-2 viral loads by cycle threshold and antigen measurements peaked on the fourth day of symptoms, with implications for testing practice. In contrast, viral loads for influenza A peaked soon after symptom onset.
Collapse
Affiliation(s)
| | - Richard Parsons
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Kaleb B. McLendon
- Emory/Children’s Laboratory for Innovative Assay Development, Department of Pathology, Emory University, Atlanta, GA USA
| | - Adrianna L. Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, GA USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA USA
| | - Greg Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA USA
| |
Collapse
|
10
|
Villafuerte-Gálvez JA, Pollock NR, Alonso CD, Chen X, Xu H, Wang L, White N, Banz A, Miller M, Daugherty K, Gonzalez-Luna AJ, Barrett C, Sprague R, Garey KW, Kelly CP. Reply to Ito. Clin Infect Dis 2023; 76:1529-1530. [PMID: 36533701 PMCID: PMC10319973 DOI: 10.1093/cid/ciac951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Affiliation(s)
- Javier A Villafuerte-Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| | - Nira R Pollock
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| | - Carolyn D Alonso
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Lamei Wang
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| | - Nicole White
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| | | | | | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| | - Anne J Gonzalez-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Caitlin Barrett
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| | - Rebecca Sprague
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Ciaran P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School via teaching hospital (BIDMC) Department of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
11
|
Banegas M, Villafuerte-Gálvez J, Paredes R, Sprague R, Barrett C, Gonzales-Luna AJ, Daugherty K, Garey KW, Xu H, Lin Q, Wang L, Chen X, Pollock NR, Kelly CP, Alonso CD. Preservation of the Innate Immune Response to Clostridioides difficile Infection in Hospitalized Immunocompromised Patients. Open Forum Infect Dis 2023; 10:ofad090. [PMID: 36949876 PMCID: PMC10026545 DOI: 10.1093/ofid/ofad090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/15/2023] [Indexed: 02/20/2023] Open
Abstract
Background Clostridioides difficile infection (CDI) immune response is influenced by the innate and adaptive (humoral) immune systems. Our prior research found attenuated humoral responses to C difficile in immunocompromised hosts (ICHs) with CDI. We sought to evaluate whether the innate immune response to CDI was influenced by ICH status. Methods We conducted a prospective study of hospitalized adults with CDI (acute diarrhea, positive C difficile stool nucleic acid amplification testing [NAAT], and decision to treat), with and without immunosuppression and measured a panel of cytokines (granulocyte colony-stimulating factor [G-CSF], interleukin [IL]-10, IL-15, IL-1β, IL-4, IL-6, IL-8, and tumor necrosis factor-α) in blood and stool at CDI diagnosis. Results were compared with measurements from a cohort of asymptomatic carrier patients (ASCs) (NAAT positive, without diarrhea) with and without immunocompromise. Results One hundred twenty-three subjects (42 ICHs, 50 non-ICHs, 31 ASCs) were included. Median values for blood and stool cytokines were similar in ICH versus non-ICH CDI subjects. In blood, G-CSF, IL-10, IL-15, IL-6, and IL-8 were higher in both groups of CDI subjects versus the ASC cohort (P < .05). In stool, IL-1β and IL-8 were higher in both groups of CDI subjects versus the ASC cohort (P < .05). Median stool concentrations of IL-1β demonstrated significant differences between the groups (ICHs, 10.97 pg/mL; non-ICHs, 9.71 pg/mL; and ASCs, 0.56 pg/mL) (P < .0001). Conclusions In this small exploratory analysis, ICH status did not significantly impact blood and fecal patterns of cytokines in humans at the diagnosis of CDI, suggesting that the innate immune response to C difficile may be conserved in immunocompromised patients.
Collapse
Affiliation(s)
- Marcela Banegas
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Javier Villafuerte-Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Rodrigo Paredes
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Rebecca Sprague
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Caitlin Barrett
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Qianyun Lin
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lamei Wang
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Nira R Pollock
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Ciarán P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Carolyn D Alonso
- Correspondence: Carolyn D. Alonso, MD, FIDSA, Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, 110 Francis St, Suite GB, Boston, MA 02215 ()
| |
Collapse
|
12
|
Rattan A, Joerger J, Williams D, Pollock NR. Similar SARS-CoV-2 Ct Value Distributions in Anterior Nares versus Nasopharyngeal Samples from Symptomatic Children during Delta and Omicron Surges. J Pediatric Infect Dis Soc 2023; 12:109-112. [PMID: 36519842 DOI: 10.1093/jpids/piac130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
In symptomatic children tested for COVID-19 by PCR during both Delta and Omicron surges, Cycle threshold value medians and distributions in anterior nares (AN) and nasopharyngeal (NP) samples were very similar, suggesting similar yield of NP and AN sampling for SARS-CoV-2 PCR testing in symptomatic children.
Collapse
Affiliation(s)
- Ankit Rattan
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jill Joerger
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - David Williams
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
13
|
Rao A, Westbrook A, Bassit L, Parsons R, Fitts E, Greenleaf M, McLendon K, Sullivan JA, O’Sick W, Baugh T, Bowers HB, Frank F, Wang E, Le M, Frediani J, Roychoudhury P, Greninger AL, Jerris R, Pollock NR, Ortlund EA, Roback JD, Lam WA, Piantadosi A. Sensitivity of Rapid Antigen Tests Against SARS-CoV-2 Omicron and Delta Variants. medRxiv 2023:2023.02.09.23285583. [PMID: 36798414 PMCID: PMC9934810 DOI: 10.1101/2023.02.09.23285583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Rapid Antigen Tests (RAT) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of eight commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR Cycle threshold (C T ) value (a proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using C T value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.
Collapse
Affiliation(s)
- Anuradha Rao
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Adrianna Westbrook
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Leda Bassit
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia
| | - Richard Parsons
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Eric Fitts
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Morgan Greenleaf
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University School of Medicine, Atlanta, GA, USA
| | - Kaleb McLendon
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
- Emory/Children's Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Julie A. Sullivan
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - William O’Sick
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
- Emory/Children's Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Tyler Baugh
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
- Emory/Children's Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Heather B. Bowers
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Ethan Wang
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mimi Le
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jennifer Frediani
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | | | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A. Ortlund
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - John D. Roback
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
- Emory/Children's Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
| | - Wilbur A. Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center at Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| |
Collapse
|
14
|
Villafuerte Gálvez JA, Pollock NR, Alonso CD, Chen X, Xu H, Wang L, White N, Banz A, Miller M, Daugherty K, Gonzalez-Luna AJ, Barrett C, Sprague R, Garey KW, Kelly CP. Stool Interleukin-1β Differentiates Clostridioides difficile Infection (CDI) From Asymptomatic Carriage and Non-CDI Diarrhea. Clin Infect Dis 2023; 76:e1467-e1475. [PMID: 35906836 PMCID: PMC10169396 DOI: 10.1093/cid/ciac624] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Despite advances in the understanding and diagnosis of Clostridioides difficile infection (CDI), clinical distinction within the colonization-infection continuum remains an unmet need. METHODS By measuring stool cytokines and antitoxin antibodies in well-characterized cohorts of CDI (diarrhea, nucleic acid amplification test [NAAT] positive), non-CDI diarrhea (NCD; diarrhea, NAAT negative), asymptomatic carriers (ASC; no diarrhea, NAAT positive) and hospital controls (CON; no diarrhea, NAAT negative), we aim to discover novel biological markers to distinguish between these cohorts. We also explore the relationship of these stool cytokines and antitoxin antibody with stool toxin concentrations and disease severity. RESULTS Stool interleukin (IL) 1β, stool immunoglobulin A (IgA), and immunoglobulin G (IgG) anti-toxin A had higher (P < .0001) concentrations in CDI (n = 120) vs ASC (n = 43), whereas toxins A, B, and fecal calprotectin did not. Areas under the receiver operating characteristic curve (ROC-AUCs) for IL-1β, IgA, and IgG anti-toxin A were 0.88, 0.83, and 0.83, respectively. A multipredictor model including IL-1β and IgA anti-toxin A achieved an ROC-AUC of 0.93. Stool IL-1β concentrations were higher in CDI compared to NCD (n = 75) (P < .0001) and NCD + ASC+ CON (CON, n = 75) (P < .0001), with ROC-AUCs of 0.83 and 0.86, respectively. Stool IL-1β had positive correlations with toxins A (ρA = +0.55) and B (ρB = +0.49) in CDI (P < .0001) but not in ASC (P > .05). CONCLUSIONS Stool concentrations of the inflammasome pathway, proinflammatory cytokine IL-1β, can accurately differentiate CDI from asymptomatic carriage and NCD, making it a promising biomarker for CDI diagnosis. Significant positive correlations exist between stool toxins and stool IL-1β in CDI but not in asymptomatic carriers.
Collapse
Affiliation(s)
- Javier A Villafuerte Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R Pollock
- Harvard Medical School, Boston, Massachusetts, USA.,Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Carolyn D Alonso
- Harvard Medical School, Boston, Massachusetts, USA.,Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Lamei Wang
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Nicole White
- Harvard Medical School, Boston, Massachusetts, USA.,Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | | | | | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Anne J Gonzalez-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Caitlin Barrett
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Rebecca Sprague
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Ciaran P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
15
|
Sandora TJ, Kociolek LK, Williams DN, Daugherty K, Geer C, Cuddemi C, Chen X, Xu H, Savage TJ, Banz A, Garey KW, Gonzales-Luna AJ, Kelly CP, Pollock NR. 883. Stool Toxin Concentrations Are Higher in Children with Baseline Severe Disease, Severe Outcomes, and Recurrence. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
In adults with C. difficile infection (CDI), higher baseline stool concentrations of toxins A and B are associated with severe baseline disease, CDI-attributable severe outcomes, and recurrence. We evaluated whether stool toxin concentration predicts these presentations in children with CDI.
Methods
We performed a prospective cohort study from 2016-2019. Participants were inpatients ≤17 years old at two pediatric hospitals with diarrhea and positive C. difficile testing who received therapy. Patients were followed for 40 days after baseline stool sample for severe outcomes (intensive care unit admission, colectomy, or death, categorized as CDI primarily attributable, CDI contributed, or CDI not contributing) and recurrence (resolution followed by new diarrhea and re-initiation of therapy). Baseline stool toxin A & B concentrations were measured using ultrasensitive single molecule array assay (cutoff for positive result = 20 pg/mL). Median baseline toxin concentrations were compared between groups using Wilcoxon tests.
Results
We enrolled 206 patients [median age 8.9 years (IQR, 4.7–13.2)]. Children with severe baseline disease by IDSA-SHEA criteria (n = 39) had higher median stool toxin A+B concentration than those without severe disease (n = 131) (2,912.6 vs. 500.5 pg/mL, P=0.05). Of the cohort, 40 (19%) had a severe outcome (4 primarily attributed to CDI, 19 with contribution from CDI, and 17 unrelated to CDI). Median toxin A+B concentration was non-significantly higher in children with a primarily-attributed severe outcome versus those without severe outcome (19,473 vs. 429.1 pg/mL, P=0.317) (Figure 1). Of 197 children with eligible data, recurrence occurred in 18 (9.1%); baseline toxin A+B concentration was significantly higher in patients with versus without recurrence (3,946.7 vs. 283.3 pg/mL, P=0.026) (Figure 2).
Conclusion
Higher stool toxin concentrations are present in children with baseline severe CDI, a CDI-attributable severe outcome, or recurrence compared with children without these presentations. Quantification of stool toxin concentration may be helpful in identifying severe CDI and predicting CDI outcomes, which could help guide decisions about clinical management.
Disclosures
Larry K. Kociolek, MD, MSCI, Merck: Grant/Research Support Timothy J. Savage, MD, MPH, MSc, UCB: Contract to Brigham and Women's Hospital Alice Banz, PhD, biomerieux: Simoa assays were performed by bioMerieux, and A.B. is an employee of bioMerieux Kevin W. Garey, PharmD, MS, Acurx: Grant/Research Support|cidara: Advisor/Consultant|cidara: Grant/Research Support|Paratek: Grant/Research Support|Seres Health: Grant/Research Support|Summit: Grant/Research Support Ciaran P. Kelly, n/a, Artugen: Advisor/Consultant|Facile Therapeutics: Advisor/Consultant|Ferring Pharma: Advisor/Consultant|Finch: Advisor/Consultant|Finch: Advisor/Consultant|First Light Biosciences: Advisor/Consultant|First Light Biosciences: Ownership Interest|Milky Way Biosciences: Advisor/Consultant|Milky Way Biosciences: Grant/Research Support|Pfizer: Advisor/Consultant|Seres Therapeutics: Advisor/Consultant|Summit Therapeutics: Advisor/Consultant.
Collapse
Affiliation(s)
| | - Larry K Kociolek
- Ann & Robert H. Lurie Children’s Hospital of Chicago , Chicago, Illinois
| | | | | | | | | | - Xinhua Chen
- Beth Israel Deaconess Medical Center , Boston, Massachusetts
| | - Hua Xu
- Beth Israel Deaconess Medical Center , Boston, Massachusetts
| | - Timothy J Savage
- Boston Children's Hospital / Brigham and Women's Hospital , Boston, Massachusetts
| | - Alice Banz
- biomerieux , Marcy L’Etoile, Auvergne , France
| | | | | | - Ciaran P Kelly
- Beth Israel Deaconess Medical Center , Boston, Massachusetts
| | | |
Collapse
|
16
|
Alonso CD, Pollock NR, Garey KW, Gonzales-Luna AJ, Williams DN, Daugherty K, Cuddemi C, Villafuerte-Gálvez J, White NC, Chen X, Xu H, Sprague R, Barrett C, Miller M, Foussadier A, Lantz A, Banz A, Kelly CP. Higher In Vivo Fecal Concentrations of Clostridioides difficile Toxins A and B in Patients With North American Pulsed-Field Gel Electrophoresis Type 1/Ribotype 027 Strain Infection. Clin Infect Dis 2022; 75:2019-2022. [PMID: 35607815 DOI: 10.1093/cid/ciac406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Indexed: 01/17/2023] Open
Abstract
Ultrasensitive, quantitative Clostridioides difficile stool toxin measurement demonstrated significantly higher concentrations of toxins A and B in patients infected with the North American pulsed-field gel electrophoresis type 1/ribotype 027 (NAP-1/027) strain compared with other strains, providing in vivo confirmation of the in vitro association between NAP-1/027 and elevated toxin production.
Collapse
Affiliation(s)
- Carolyn D Alonso
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R Pollock
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - David N Williams
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Christine Cuddemi
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Javier Villafuerte-Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Nicole C White
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Rebecca Sprague
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Caitlin Barrett
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | | | | | | | | | - Ciarán P Kelly
- Harvard Medical School, Boston, Massachusetts, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| |
Collapse
|
17
|
Krüger LJ, Lindner AK, Gaeddert M, Tobian F, Klein J, Steinke S, Lainati F, Schnitzler P, Nikolai O, Mockenhaupt FP, Seybold J, Corman VM, Jones TC, Pollock NR, Knorr B, Welker A, Weber S, Sethurarnan N, Swaminathan J, Solomon H, Padmanaban A, Thirunarayan M, L P, de Vos M, Ongarello S, Sacks JA, Escadafal C, Denkinger CM. A Multicenter Clinical Diagnostic Accuracy Study of SureStatus, an Affordable, WHO Emergency Use-Listed, Rapid, Point-Of-Care Antigen-Detecting Diagnostic Test for SARS-CoV-2. Microbiol Spectr 2022; 10:e0122922. [PMID: 36066256 PMCID: PMC9604065 DOI: 10.1128/spectrum.01229-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/04/2022] [Indexed: 12/30/2022] Open
Abstract
Access to reverse transcription-PCR (RT-PCR) testing, the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection, is limited throughout the world, due to restricted resources, available infrastructure, and high costs. Antigen-detecting rapid diagnostic tests (Ag-RDTs) overcome some of these barriers, but independent clinical validations in settings of intended use are scarce. To inform the World Health Organization's (WHO) emergency use listing (EUL) procedure and ensure affordable, high-quality Ag-RDTs, we assessed the performance and ease of use of the SureStatus for SARS-CoV-2. For this prospective, multicenter diagnostic accuracy study, we recruited unvaccinated participants with presumed SARS-CoV-2 infection in India and Germany from December 2020 to March 2021, when the Alpha (B.1.1.7) variant was predominantly circulating. Paired swabs were performed for (i) routine clinical RT-PCR testing (sampling was either nasopharyngeal [NP] or combined NP and oropharyngeal [NP/OP]) and (ii) Ag-RDT (sampling was NP). Performance of the Ag-RDT was compared to RT-PCR overall and by predefined subgroups, e.g., cycle threshold (CT) value, symptoms, and days from symptom onset. To understand the usability, a system usability scale (SUS) questionnaire and ease-of-use (EoU) assessment were performed. A total of 1,119 participants were included in the analysis, of whom 205 (18.3%) were RT-PCR positive. SureStatus detected 169 out of 205 RT-PCR-positive participants, reporting a sensitivity of 82.4% (95% confidence interval [CI]: 76.6% to 87.1%) and a specificity of 98.5% (95% CI: 97.4% to 99.1%). In the first 7 days post-symptom onset, the sensitivity was 90.7% (95% CI: 83.5% to 94.9%), when CT values were low and viral loads were high. The test was characterized as easy to use (SUS, 85/100) and considered suitable for point-of-care settings, although quality concerns were raised due to visibly contaminated packaging of swabs included in the test kits. The SureStatus diagnostic test can be considered a reliable test during the first week of SARS-CoV-2 infection, with high sensitivity in combination with excellent usability. IMPORTANCE Our manufacturer-independent, prospective diagnostic accuracy study assessed clinical performance in participants presumed to have a SARS-CoV-2 infection at three study sites in two countries. We assessed the accuracy overall and in predefined subgroups (CT values and symptom duration). SureStatus performed with high sensitivity. Its sensitivity was particularly high in the first 3 days after symptom onset and when CT values were low (i.e., the viral load was high). The system usability and ease-of-use assessment complements the accuracy assessment of the test and highlights critical factors to facilitate the widespread use of SureStatus in point-of-care settings. The high sensitivity demonstrated by the evaluated Ag-RDT within the first days of symptoms, when most transmission occurs, supports the role of Ag-RDTs for public health-relevant screening. Evidence from this study was used to inform the World Health Organization Emergency Use Listing procedure.
Collapse
Affiliation(s)
- Lisa J. Krüger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas K. Lindner
- Charité—Universitätsmedizin Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Mary Gaeddert
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Tobian
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Julian Klein
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Salome Steinke
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Federica Lainati
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Paul Schnitzler
- Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olga Nikolai
- Charité—Universitätsmedizin Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Frank P. Mockenhaupt
- Charité—Universitätsmedizin Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Joachim Seybold
- Charité—Universitätsmedizin Berlin, Medical Directorate, Berlin, Germany
| | - Victor M. Corman
- Charité—Universitätsmedizin Berlin, Institute of Virology, Berlin, Germany
- German Center for Infection Research (DZIF), Charité Partner Site, Berlin, Germany
| | - Terry C. Jones
- Charité—Universitätsmedizin Berlin, Institute of Virology, Berlin, Germany
- German Center for Infection Research (DZIF), Charité Partner Site, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Britta Knorr
- Department of Public Health Rhein Neckar Region, Heidelberg, Germany
| | - Andreas Welker
- Department of Public Health Rhein Neckar Region, Heidelberg, Germany
| | | | | | | | | | | | | | - Prabakaran L
- Foundation of Innovative New Diagnostics (FIND), New Delhi, India
| | - Margaretha de Vos
- Foundation of Innovative New Diagnostics (FIND), Campus Biotech, Geneva, Switzerland
| | - Stefano Ongarello
- Foundation of Innovative New Diagnostics (FIND), Campus Biotech, Geneva, Switzerland
| | - Jilian A. Sacks
- Foundation of Innovative New Diagnostics (FIND), Campus Biotech, Geneva, Switzerland
| | - Camille Escadafal
- Foundation of Innovative New Diagnostics (FIND), Campus Biotech, Geneva, Switzerland
| | - Claudia M. Denkinger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg University Hospital Partner Site, Heidelberg, Germany
| |
Collapse
|
18
|
Sigal GB, Novak T, Mathew A, Chou J, Zhang Y, Manjula N, Bathala P, Joe J, Padmanabhan N, Romero D, Allegri-Machado G, Joerger J, Loftis LL, Schwartz SP, Walker TC, Fitzgerald JC, Tarquinio KM, Zinter MS, Schuster JE, Halasa NB, Cullimore ML, Maddux AB, Staat MA, Irby K, Flori HR, Coates BM, Crandall H, Gertz SJ, Randolph AG, Pollock NR. Measurement of Severe Acute Respiratory Syndrome Coronavirus 2 Antigens in Plasma of Pediatric Patients With Acute Coronavirus Disease 2019 or Multisystem Inflammatory Syndrome in Children Using an Ultrasensitive and Quantitative Immunoassay. Clin Infect Dis 2022; 75:1351-1358. [PMID: 35213684 PMCID: PMC8903440 DOI: 10.1093/cid/ciac160] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens in blood has high sensitivity in adults with acute coronavirus disease 2019 (COVID-19), but sensitivity in pediatric patients is unclear. Recent data suggest that persistent SARS-CoV-2 spike antigenemia may contribute to multisystem inflammatory syndrome in children (MIS-C). We quantified SARS-CoV-2 nucleocapsid (N) and spike (S) antigens in blood of pediatric patients with either acute COVID-19 or MIS-C using ultrasensitive immunoassays (Meso Scale Discovery). METHODS Plasma was collected from inpatients (<21 years) enrolled across 15 hospitals in 15 US states. Acute COVID-19 patients (n = 36) had a range of disease severity and positive nasopharyngeal SARS-CoV-2 RT-PCR within 24 hours of blood collection. Patients with MIS-C (n = 53) met CDC criteria and tested positive for SARS-CoV-2 (RT-PCR or serology). Controls were patients pre-COVID-19 (n = 67) or within 24 hours of negative RT-PCR (n = 43). RESULTS Specificities of N and S assays were 95-97% and 100%, respectively. In acute COVID-19 patients, N/S plasma assays had 89%/64% sensitivity; sensitivities in patients with concurrent nasopharyngeal swab cycle threshold (Ct) ≤35 were 93%/63%. Antigen concentrations ranged from 1.28-3844 pg/mL (N) and 1.65-1071 pg/mL (S) and correlated with disease severity. In MIS-C, antigens were detected in 3/53 (5.7%) samples (3 N-positive: 1.7, 1.9, 121.1 pg/mL; 1 S-positive: 2.3 pg/mL); the patient with highest N had positive nasopharyngeal RT-PCR (Ct 22.3) concurrent with blood draw. CONCLUSIONS Ultrasensitive blood SARS-CoV-2 antigen measurement has high diagnostic yield in children with acute COVID-19. Antigens were undetectable in most MIS-C patients, suggesting that persistent antigenemia is not a common contributor to MIS-C pathogenesis.
Collapse
Affiliation(s)
| | - Tanya Novak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, and Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, USA
| | - Anu Mathew
- Meso Scale Diagnostics, LLC, Rockville, Maryland, USA
| | - Janet Chou
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Yubo Zhang
- Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | | | | | - Jessica Joe
- Meso Scale Diagnostics, LLC, Rockville, Maryland, USA
| | | | - Daniel Romero
- Meso Scale Diagnostics, LLC, Rockville, Maryland, USA
| | | | - Jill Joerger
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Laura L Loftis
- Division of Critical Care Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Stephanie P Schwartz
- Department of Pediatrics, University of North Carolina at Chapel Hill Children’s Hospital, Chapel Hill, North Carolina, USA
| | - Tracie C Walker
- Department of Pediatrics, University of North Carolina at Chapel Hill Children’s Hospital, Chapel Hill, North Carolina, USA
| | - Julie C Fitzgerald
- Division of Critical Care, Department of Anesthesiology and Critical Care, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Keiko M Tarquinio
- Division of Critical Care Medicine, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Matt S Zinter
- Divisions of Critical Care and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Jennifer E Schuster
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Natasha B Halasa
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Melissa L Cullimore
- Department of Pediatrics, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Aline B Maddux
- Department of Pediatrics, Section of Critical Care Medicine, University of Colorado School of Medicine and Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Mary A Staat
- Department of Pediatrics, University of Cincinnati, Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Katherine Irby
- Section of Pediatric Critical Care, Department of Pediatrics, Arkansas Children’s Hospital, Little Rock, Arkansas, USA
| | - Heidi R Flori
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Mott Children’s Hospital and University of Michigan, Ann Arbor, Michigan, USA
| | - Bria M Coates
- Division of Critical Care Medicine, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Hillary Crandall
- Division of Pediatric Critical Care, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Shira J Gertz
- Division of Pediatric Critical Care, Department of Pediatrics, Saint Barnabas Medical Center, Livingston, New Jersey, USA
| | - Adrienne G Randolph
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, and Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | |
Collapse
|
19
|
Cao Y, Wang L, Ke S, Kelly CP, Pollock NR, Villafuerte Gálvez JA, Daugherty K, Xu H, Yao J, Chen Y, Liu YY, Chen X. Analysis of Intestinal Mycobiota of Patients with Clostridioides difficile Infection among a Prospective Inpatient Cohort. Microbiol Spectr 2022; 10:e0136222. [PMID: 35867408 PMCID: PMC9430669 DOI: 10.1128/spectrum.01362-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/23/2022] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) is a burden to health care systems worldwide. Gut microbiota dysbiosis associated with CDI has been well accepted. However, contribution of fungal mycobiota to CDI has recently gained research interest. Here, we report the gut mycobiota composition of 149 uniquely well characterized participants from a prospective clinical cohort and evaluate the discriminating ability of gut mycobiota to classify CDI and non-CDI patients. Fecal samples were divided into two groups: (i) CDI (inpatients who had clinically significant diarrhea and positive nucleic acid amplification testing [NAAT] and received subsequent CDI therapy, n = 58) and (ii) non-CDI, which can be further divided into three subgroups: (a) carrier (inpatients with positive stool NAAT but without diarrhea; n = 28); (b) diarrhea (inpatients with negative stool NAAT; n = 31); and (c) control (inpatients with negative stool NAAT and without diarrhea; n = 32). Fecal mycobiota composition was analyzed by internal transcribed spacer 2 (ITS2) sequencing. In comparison to non-CDI patients, CDI patients tend to have gut mycobiota with lower biodiversity, weaker fungi correlations, and weaker correlations between fungi and host immune factors. Notably, 11 genera (Saccharomyces, Penicillium, Aspergillus, Cystobasidium, Cladosporium, and so on) were significantly enriched in non-CDI patients, and Pichia and Suhomyces were enriched in patients with CDI, while 1 two genera, Cystobasidium and Exophiala, had higher abundance in patients with diarrhea compared with CDI (linear discriminant analysis [LDA] > 3.0; P < 0.05). Ascomycota and Basidiomycota (or Candida and Saccharomyces) exhibited a strong negative correlation (r ≤ -0.714 or r ≤ -0.387; P < 0.05), and the ratios of Ascomycota to Basidiomycota or genera Candida to Saccharomyces were dramatically higher in CDI patients than in non-CDI patients (P < 0.05). A disease-specific pattern with much weaker fungal abundance correlations was observed in the CDI group compared to that in the non-CDI and diarrhea groups, suggesting that these correlations may contribute to the development of CDI. Our findings provided specific markers of stool fungi that distinguish CDI from all non-CDI hospitalized patients. This study's potential clinical utility for better CDI diagnosis warrants further investigation. IMPORTANCE Clostridioides difficile is an opportunistic bacterial pathogen that causes a serious and potentially life-threatening infection of the human gut. It remains an existing challenge to distinguish active infection of CDI from diarrhea with non-CDI causes. A few large prospective studies from recent years suggest that there is no single optimal test for the diagnosis of CDI. Previous research has concentrated on the relationship between bacteria and CDI, while the roles of fungi, as a significant proportion of the gut microbial ecosystem, remain understudied. In this study, we report a series of fungal markers that may add diagnostic values for the development of a more systematic approach to accurate CDI diagnosis. These results help open the door for better understanding of the relationship between host immune factors and the fungal community in the context of CDI pathogenesis.
Collapse
Affiliation(s)
- Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Lamei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ciarán P. Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R. Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Javier A. Villafuerte Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
20
|
Sandora TJ, Williams DN, Daugherty K, Geer C, Cuddemi C, Kociolek LK, Chen X, Xu H, Savage TJ, Banz A, Garey KW, Gonzales-Luna AJ, Kelly CP, Pollock NR. Stool Toxin Concentration Does Not Distinguish Clostridioides difficile Infection from Colonization in Children Less Than 3 Years of Age. J Pediatric Infect Dis Soc 2022; 11:454-458. [PMID: 35801632 PMCID: PMC9595052 DOI: 10.1093/jpids/piac059] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 06/10/2022] [Indexed: 11/14/2022]
Abstract
In a prospective cohort study, stools from children <3 years with and without diarrhea who were Clostridioides difficile nucleic acid amplification test-positive underwent ultrasensitive and quantitative toxin measurement. Among 37 cases and 46 controls, toxin concentration distributions overlapped substantially. Toxin concentration alone does not distinguish C. difficile infection from colonization in young children.
Collapse
Affiliation(s)
- Thomas J Sandora
- Corresponding Author: Thomas J. Sandora, MD MPH, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA. E-mail:
| | - David N Williams
- Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine Geer
- Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, Massachusetts, USA,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine Cuddemi
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Larry K Kociolek
- Division of Infectious Diseases, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Timothy J Savage
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Ciarán P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
21
|
Farmer S, Razin V, Peagler AF, Strickler S, Fain WB, Damhorst GL, Kempker RR, Pollock NR, Brand O, Seitter B, Heilman SS, Nehl EJ, Levy JM, Gottfried DS, Martin GS, Greenleaf M, Ku DN, Waggoner JJ, Iffrig E, Mannino RG, F. Wang Y, Ortlund E, Sullivan J, Rebolledo PA, Clavería V, Roback JD, Benoit M, Stone C, Esper A, Frank F, Lam WA. Don't forget about human factors: Lessons learned from COVID-19 point-of-care testing. Cell Rep Methods 2022; 2:100222. [PMID: 35527805 PMCID: PMC9061138 DOI: 10.1016/j.crmeth.2022.100222] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
During the COVID-19 pandemic, the development of point-of-care (POC) diagnostic testing accelerated in an unparalleled fashion. As a result, there has been an increased need for accurate, robust, and easy-to-use POC testing in a variety of non-traditional settings (i.e., pharmacies, drive-thru sites, schools). While stakeholders often express the desire for POC technologies that are "as simple as digital pregnancy tests," there is little discussion of what this means in regards to device design, development, and assessment. The design of POC technologies and systems should take into account the capabilities and limitations of the users and their environments. Such "human factors" are important tenets that can help technology developers create POC technologies that are effective for end-users in a multitude of settings. Here, we review the core principles of human factors and discuss lessons learned during the evaluation process of SARS-CoV-2 POC testing.
Collapse
Affiliation(s)
- Sarah Farmer
- Center for Advanced Communications Policy, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, GA, USA
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
| | - Victoria Razin
- Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, GA, USA
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
| | - Amanda Foster Peagler
- Center for Advanced Communications Policy, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, GA, USA
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
| | - Samantha Strickler
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Emergency Medicine and Department of Anesthesia, Division of Critical Care, Emory University School of Medicine, Atlanta, GA, USA
| | - W. Bradley Fain
- Center for Advanced Communications Policy, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, GA, USA
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
| | - Gregory L. Damhorst
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Russell R. Kempker
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Nira R. Pollock
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Oliver Brand
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brooke Seitter
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Stacy S. Heilman
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric J. Nehl
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Joshua M. Levy
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Otolaryngology-Head and Neck Surgery, Emory University School of Medicine, Atlanta, GA, USA
| | - David S. Gottfried
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Greg S. Martin
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Morgan Greenleaf
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
| | - David N. Ku
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jesse J. Waggoner
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth Iffrig
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Robert G. Mannino
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yun F. Wang
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric Ortlund
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Julie Sullivan
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Paulina A. Rebolledo
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Viviana Clavería
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - John D. Roback
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - MacArthur Benoit
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Cheryl Stone
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Annette Esper
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Filipp Frank
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Wilbur A. Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| |
Collapse
|
22
|
Brümmer LE, Katzenschlager S, McGrath S, Schmitz S, Gaeddert M, Erdmann C, Bota M, Grilli M, Larmann J, Weigand MA, Pollock NR, Macé A, Erkosar B, Carmona S, Sacks JA, Ongarello S, Denkinger CM. Accuracy of rapid point-of-care antigen-based diagnostics for SARS-CoV-2: An updated systematic review and meta-analysis with meta-regression analyzing influencing factors. PLoS Med 2022; 19:e1004011. [PMID: 35617375 PMCID: PMC9187092 DOI: 10.1371/journal.pmed.1004011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/10/2022] [Accepted: 05/04/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Comprehensive information about the accuracy of antigen rapid diagnostic tests (Ag-RDTs) for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is essential to guide public health decision makers in choosing the best tests and testing policies. In August 2021, we published a systematic review and meta-analysis about the accuracy of Ag-RDTs. We now update this work and analyze the factors influencing test sensitivity in further detail. METHODS AND FINDINGS We registered the review on PROSPERO (registration number: CRD42020225140). We systematically searched preprint and peer-reviewed databases for publications evaluating the accuracy of Ag-RDTs for SARS-CoV-2 until August 31, 2021. Descriptive analyses of all studies were performed, and when more than 4 studies were available, a random-effects meta-analysis was used to estimate pooled sensitivity and specificity with reverse transcription polymerase chain reaction (RT-PCR) testing as a reference. To evaluate factors influencing test sensitivity, we performed 3 different analyses using multivariable mixed-effects meta-regression models. We included 194 studies with 221,878 Ag-RDTs performed. Overall, the pooled estimates of Ag-RDT sensitivity and specificity were 72.0% (95% confidence interval [CI] 69.8 to 74.2) and 98.9% (95% CI 98.6 to 99.1). When manufacturer instructions were followed, sensitivity increased to 76.3% (95% CI 73.7 to 78.7). Sensitivity was markedly better on samples with lower RT-PCR cycle threshold (Ct) values (97.9% [95% CI 96.9 to 98.9] and 90.6% [95% CI 88.3 to 93.0] for Ct-values <20 and <25, compared to 54.4% [95% CI 47.3 to 61.5] and 18.7% [95% CI 13.9 to 23.4] for Ct-values ≥25 and ≥30) and was estimated to increase by 2.9 percentage points (95% CI 1.7 to 4.0) for every unit decrease in mean Ct-value when adjusting for testing procedure and patients' symptom status. Concordantly, we found the mean Ct-value to be lower for true positive (22.2 [95% CI 21.5 to 22.8]) compared to false negative (30.4 [95% CI 29.7 to 31.1]) results. Testing in the first week from symptom onset resulted in substantially higher sensitivity (81.9% [95% CI 77.7 to 85.5]) compared to testing after 1 week (51.8%, 95% CI 41.5 to 61.9). Similarly, sensitivity was higher in symptomatic (76.2% [95% CI 73.3 to 78.9]) compared to asymptomatic (56.8% [95% CI 50.9 to 62.4]) persons. However, both effects were mainly driven by the Ct-value of the sample. With regards to sample type, highest sensitivity was found for nasopharyngeal (NP) and combined NP/oropharyngeal samples (70.8% [95% CI 68.3 to 73.2]), as well as in anterior nasal/mid-turbinate samples (77.3% [95% CI 73.0 to 81.0]). Our analysis was limited by the included studies' heterogeneity in viral load assessment and sample origination. CONCLUSIONS Ag-RDTs detect most of the individuals infected with SARS-CoV-2, and almost all (>90%) when high viral loads are present. With viral load, as estimated by Ct-value, being the most influential factor on their sensitivity, they are especially useful to detect persons with high viral load who are most likely to transmit the virus. To further quantify the effects of other factors influencing test sensitivity, standardization of clinical accuracy studies and access to patient level Ct-values and duration of symptoms are needed.
Collapse
Affiliation(s)
- Lukas E. Brümmer
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Sean McGrath
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Stephani Schmitz
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mary Gaeddert
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Marc Bota
- Agaplesion Bethesda Hospital, Hamburg, Germany
| | - Maurizio Grilli
- Library, University Medical Center Mannheim, Mannheim, Germany
| | - Jan Larmann
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus A. Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | | | | | | | | | | | - Claudia M. Denkinger
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), partner site Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
23
|
Westbrook AL, Benedit LC, Frediani JK, Griffiths MA, Khan NY, Levy JM, Morris CR, Rostad CA, Stone CL, Sullivan J, Vos MB, Welsh J, Wood A, Martin GS, Lam W, Pollock NR. Predictive value of isolated symptoms for diagnosis of SARS-CoV-2 infection in children tested during peak circulation of the delta variant. Clin Infect Dis 2022; 75:1131-1139. [PMID: 35271694 PMCID: PMC8992302 DOI: 10.1093/cid/ciac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Indexed: 01/03/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) testing policies for symptomatic children attending US schools or daycare vary, and whether isolated symptoms should prompt testing is unclear. We evaluated children presenting for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing to determine if the likelihood of having a positive SARS-CoV-2 test differed between participants with 1 symptom vs ≥2 symptoms, and to examine the predictive capability of isolated symptoms. Methods Participants aged <18 years presenting for clinical SARS-CoV-2 molecular testing in 6 sites in urban/suburban/rural Georgia (July–October, 2021; Delta variant predominant) were queried about individual symptoms. Participants were classified into 3 groups: asymptomatic, 1 symptom only, or ≥2 symptoms. SARS-CoV-2 test results and clinical characteristics of the 3 groups were compared. Sensitivity, specificity, positive predictive values (PPVs), and negative predictive values (NPVs) for isolated symptoms were calculated by fitting a saturated Poisson model. Results Of 602 participants, 21.8% tested positive and 48.7% had a known or suspected close contact. Children reporting 1 symptom (n = 82; odds ratio [OR], 6.00 [95% confidence interval {CI}, 2.70–13.33]) and children reporting ≥2 symptoms (n = 365; OR, 5.25 [95% CI, 2.66–10.38]) were significantly more likely to have a positive COVID-19 test than asymptomatic children (n = 155), but they were not significantly different from each other (OR, 0.88 [95% CI, .52–1.49]). Sensitivity and PPV were highest for isolated fever (33% and 57%, respectively), cough (25% and 32%), and sore throat (21% and 45%); headache had low sensitivity (8%) but higher PPV (33%). Sensitivity and PPV of isolated congestion/rhinorrhea were 8% and 9%, respectively. Conclusions With high Delta variant prevalence, children with isolated symptoms were as likely as those with multiple symptoms to test positive for COVID-19. Isolated fever, cough, sore throat, or headache, but not congestion/rhinorrhea, offered the highest predictive value.
Collapse
Affiliation(s)
- Adrianna L Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, GA USA
| | - Laura C Benedit
- Department of Clinical Research, Children's Healthcare of Atlanta, Atlanta, GA USA
| | | | - Mark A Griffiths
- Children's Healthcare of Atlanta, Atlanta, GA USA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
| | - Nabeel Y Khan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
| | - Joshua M Levy
- Department of Otolaryngology-HNS, Emory University School of Medicine, Atlanta, GA USA
| | - Claudia R Morris
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA.,Division of Pediatric Emergency Medicine, Children's Healthcare of Atlanta, Atlanta, GA USA
| | - Christina A Rostad
- Children's Healthcare of Atlanta, Atlanta, GA USA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
| | - Cheryl L Stone
- Department of Clinical Research, Children's Healthcare of Atlanta, Atlanta, GA USA
| | - Julie Sullivan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
| | - Miriam B Vos
- Children's Healthcare of Atlanta, Atlanta, GA USA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
| | - Jean Welsh
- Children's Healthcare of Atlanta, Atlanta, GA USA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
| | - Anna Wood
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, GA USA
| | - Greg S Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA.,Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Atlanta, GA USA.,Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA USA
| |
Collapse
|
24
|
Lin J, Frediani JK, Damhorst GL, Sullivan JA, Westbrook A, McLendon K, Baugh TJ, O'Sick WH, Roback JD, Piantadosi AL, Waggoner JJ, Bassit L, Rao A, Greenleaf M, O'Neal JW, Swanson S, Pollock NR, Martin GS, Lam WA, Levy JM. Where is Omicron? Comparison of SARS-CoV-2 RT-PCR and Antigen Test Sensitivity at Commonly Sampled Anatomic Sites Over the Course of Disease. medRxiv 2022. [PMID: 35169808 DOI: 10.1101/2022.02.08.22270685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Upper respiratory samples for SARS-CoV-2 detection include the gold standard nasopharyngeal (NP) swab, and mid-turbinate (MT) nasal swabs, oropharyngeal (OP) swabs, and saliva. Following the emergence of the omicron (B.1.1.529) variant, limited preliminary data suggest that OP swabs or saliva samples may be more sensitive than nasal swabs, highlighting the need to understand differences in viral load across different sites. METHODS MT, OP, and saliva samples were collected from symptomatic individuals presenting for evaluation in Atlanta, GA, in January 2022. Longitudinal samples were collected from a family cohort following COVID-19 exposure to describe detection of viral targets over the course of infection. RESULTS SARS-CoV-2 RNA and nucleocapsid antigen measurements demonstrated a nares-predominant phenotype in a familial cohort. A consistent dominant location for SARS-CoV-2 was not found among 54 individuals. Positive percent agreement for virus detection in MT, OP and saliva specimens were 66.7 [54.1-79.2], 82.2 [71.1-93.4], and 72.5 [60.3-84.8] by RT-PCR, respectively, and 46.2 [32.6-59.7], 51.2 [36.2-66.1], and 72.0 [59.6-84.4] by ultrasensitive antigen assay. The composite of positive MT or OP assay was not significantly different than either alone for both RT-PCR and antigen assay (PPA 86.7 [76.7-96.6] and 59.5 [44.7-74.4], respectively). CONCLUSIONS Our data suggest that SARS-CoV-2 nucleocapsid and RNA exhibited similar kinetics and diagnostic yield in three upper respiratory sample types across the duration of symptomatic disease. Collection of OP or combined nasal and OP samples does not appear to increase sensitivity versus validated nasal sampling for rapid detection of viral antigen.
Collapse
|
25
|
Krüger LJ, Tanuri A, Lindner AK, Gaeddert M, Köppel L, Tobian F, Brümmer LE, Klein JAF, Lainati F, Schnitzler P, Nikolai O, Mockenhaupt FP, Seybold J, Corman VM, Jones TC, Drosten C, Gottschalk C, Weber SF, Weber S, Ferreira OC, Mariani D, Dos Santos Nascimento ER, Pereira Pinto Castineiras TM, Galliez RM, Faffe DS, Leitão IDC, Dos Santos Rodrigues C, Frauches TS, Nocchi KJCV, Feitosa NM, Ribeiro SS, Pollock NR, Knorr B, Welker A, de Vos M, Sacks J, Ongarello S, Denkinger CM. Accuracy and ease-of-use of seven point-of-care SARS-CoV-2 antigen-detecting tests: A multi-centre clinical evaluation. EBioMedicine 2022; 75:103774. [PMID: 34959134 PMCID: PMC8702380 DOI: 10.1016/j.ebiom.2021.103774] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Antigen-detecting rapid diagnostic tests (Ag-RDTs) for SARS-CoV-2 are important diagnostic tools. We assessed clinical performance and ease-of-use of seven Ag-RDTs in a prospective, manufacturer-independent, multi-centre cross-sectional diagnostic accuracy study to inform global decision makers. METHODS Unvaccinated participants suspected of a first SARS-CoV-2 infection were recruited at six sites (Germany, Brazil). Ag-RDTs were evaluated sequentially, with collection of paired swabs for routine reverse transcription polymerase chain reaction (RT-PCR) testing and Ag-RDT testing. Performance was compared to RT-PCR overall and in sub-group analyses (viral load, symptoms, symptoms duration). To understandusability a System Usability Scale (SUS) questionnaire and ease-of-use (EoU) assessment were performed. FINDINGS 7471 participants were included in the analysis. Sensitivities across Ag-RDTs ranged from 70·4%-90·1%, specificities were above 97·2% for all Ag-RDTs but one (93·1%).Ag-RDTs, Mologic, Bionote, Standard Q, showed diagnostic accuracy in line with WHO targets (> 80% sensitivity, > 97% specificity). All tests showed high sensitivity in the first three days after symptom onset (≥87·1%) and in individuals with viral loads≥ 6 log10SARS-CoV2 RNA copies/mL (≥ 88·7%). Usability varied, with Rapigen, Bionote and Standard Q reaching very good scores; 90, 88 and 84/100, respectively. INTERPRETATION Variability in test performance is partially explained by variable viral loads in population evaluated over the course of the pandemic. All Ag-RDTs reach high sensitivity early in the disease and in individuals with high viral loads, supporting their role in identifying transmission relevant infections. For easy-to-use tests, performance shown will likely be maintained in routine implementation. FUNDING Ministry of Science, Research and Arts, State of Baden-Wuerttemberg, Germany, internal funds from Heidelberg University Hospital, University Hospital Charité - Universitätsmedizin Berlin, UK Department of International Development, WHO, Unitaid.
Collapse
Affiliation(s)
- Lisa J Krüger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Instituto de Biologia - Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Andreas K Lindner
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Augustenburger Pl. 1, Berlin 13353, Germany
| | - Mary Gaeddert
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Lisa Köppel
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Frank Tobian
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Lukas E Brümmer
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Julian A F Klein
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Federica Lainati
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Paul Schnitzler
- Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Olga Nikolai
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Augustenburger Pl. 1, Berlin 13353, Germany
| | - Frank P Mockenhaupt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Augustenburger Pl. 1, Berlin 13353, Germany
| | - Joachim Seybold
- Medical Directorate, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Pl. 1, Berlin 13353, Germany
| | - Victor M Corman
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Rahel-Hirsch-Weg 3, Berlin 10117, Germany; German Centre for Infection Research (DZIF), Partner Site Charité, Charitépl. 1, Berlin 10117, Germany
| | - Terence C Jones
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Rahel-Hirsch-Weg 3, Berlin 10117, Germany; German Centre for Infection Research (DZIF), Partner Site Charité, Charitépl. 1, Berlin 10117, Germany; Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Rahel-Hirsch-Weg 3, Berlin 10117, Germany; German Centre for Infection Research (DZIF), Partner Site Charité, Charitépl. 1, Berlin 10117, Germany
| | - Claudius Gottschalk
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Stefan F Weber
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Stephan Weber
- Acomed Statistik, Fockestraße 57, Leipzig 04275, Germany
| | - Orlando C Ferreira
- Laboratório de Virologia Molecular, Instituto de Biologia - Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Diana Mariani
- Laboratório de Virologia Molecular, Instituto de Biologia - Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Erika Ramos Dos Santos Nascimento
- Laboratório de Virologia Molecular, Instituto de Biologia - Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Terezinha M Pereira Pinto Castineiras
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Rafael Mello Galliez
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Debora Souza Faffe
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Isabela de Carvalho Leitão
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Claudia Dos Santos Rodrigues
- Serviço de Atendimento Especializado / Centro de Testagem e Aconselhamento, Avenida Roberto Silveira, 46 - 3° Andar, Maricá, Brazil
| | - Thiago Silva Frauches
- Laboratório Central Dr. Francisco Rímolo Neto, R. Álvares de Castro, n° 346, Maricá, RJ 24900-880, Brazil
| | | | - Natalia Martins Feitosa
- Instituto de Biodiversidade e Sustantabilidade NUPEM, Universidade Federal do Rio de Janeiro, Campus Macaé, Av. São José Barreto, 764 - São José do Barreto, Macaé, RJ 27965-045, Brazil
| | - Sabrina Santana Ribeiro
- Secretaria Municipal de Saúde de Guapimirim, Rua Pastor Francisco Antônio Rosa - S/N, Guapimirim, RJ 25946-253, Brazil
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, United States
| | - Britta Knorr
- Department Public Health Rhein Neckar Region, Kurfürsten-Anlage 38-40, Heidelberg 69115, Germany
| | - Andreas Welker
- Department Public Health Rhein Neckar Region, Kurfürsten-Anlage 38-40, Heidelberg 69115, Germany
| | - Margaretha de Vos
- FIND, Campus Biotech, Building B, Level 0, Chemin des Mines 9, Geneva 1202, Switzerland
| | - JilianA Sacks
- FIND, Campus Biotech, Building B, Level 0, Chemin des Mines 9, Geneva 1202, Switzerland
| | - Stefano Ongarello
- FIND, Campus Biotech, Building B, Level 0, Chemin des Mines 9, Geneva 1202, Switzerland
| | - Claudia M Denkinger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg University Hospital, Im Neuenheimer Feld 672, Heidelberg 69120, Germany.
| |
Collapse
|
26
|
Sigal GB, Novak T, Mathew A, Chou J, Zhang Y, Manjula N, Bathala P, Joe J, Padmanabhan N, Romero D, Allegri-Machado G, Joerger J, Loftis LL, Schwartz SP, Walker TC, Fitzgerald JC, Tarquinio KM, Zinter MS, Schuster JE, Halasa NB, Cullimore ML, Maddux AB, Staat MA, Irby K, Flori HR, Coates BM, Crandall H, Gertz SJ, Randolph AG, Pollock NR. Measurement of SARS-CoV-2 antigens in plasma of pediatric patients with acute COVID-19 or MIS-C using an ultrasensitive and quantitative immunoassay. medRxiv 2021:2021.12.08.21267502. [PMID: 34909787 PMCID: PMC8669854 DOI: 10.1101/2021.12.08.21267502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Detection of SARS-CoV-2 antigens in blood has high sensitivity in adults with acute COVID-19, but sensitivity in pediatric patients is unclear. Recent data suggest that persistent SARS-CoV-2 spike antigenemia may contribute to multisystem inflammatory syndrome in children (MIS-C). We quantified SARS-CoV-2 nucleocapsid (N) and spike (S) antigens in blood of pediatric patients with either acute COVID-19 or MIS-C using ultrasensitive immunoassays (Meso Scale Discovery). METHODS Plasma was collected from inpatients (<21 years) enrolled across 15 hospitals in 15 US states. Acute COVID-19 patients (n=36) had a range of disease severity and positive nasopharyngeal SARS-CoV-2 RT-PCR within 24 hours of blood collection. Patients with MIS-C (n=53) met CDC criteria and tested positive for SARS-CoV-2 (RT-PCR or serology). Controls were patients pre-COVID-19 (n=67) or within 24h of negative RT-PCR (n=43). RESULTS Specificities of N and S assays were 95-97% and 100%, respectively. In acute COVID-19 patients, N/S plasma assays had 89%/64% sensitivity, respectively; sensitivity in patients with concurrent nasopharyngeal swab cycle threshold (Ct) ≤ 35 were 93%/63%. Antigen concentrations ranged from 1.28-3,844 pg/mL (N) and 1.65-1,071 pg/mL (S) and correlated with disease severity. In MIS-C, antigens were detected in 3/53 (5.7%) samples (3 N-positive: 1.7, 1.9, 121.1 pg/mL; 1 S-positive: 2.3 pg/mL); the patient with highest N had positive nasopharyngeal RT-PCR (Ct 22.3) concurrent with blood draw. CONCLUSIONS Ultrasensitive blood SARS-CoV-2 antigen measurement has high diagnostic yield in children with acute COVID-19. Antigens were undetectable in most MIS-C patients, suggesting that persistent antigenemia is not a common contributor to MIS-C pathogenesis. KEY POINTS In a U.S. pediatric cohort tested with ultrasensitive immunoassays, SARS-CoV-2 nucleocapsid antigens were detectable in most patients with acute COVID-19, and spike antigens were commonly detectable. Both antigens were undetectable in almost all MIS-C patients.
Collapse
Affiliation(s)
| | - Tanya Novak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital and Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Anu Mathew
- Meso Scale Diagnostics, LLC., Rockville, MD, USA
| | - Janet Chou
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Yubo Zhang
- Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, MA, USA
| | | | | | - Jessica Joe
- Meso Scale Diagnostics, LLC., Rockville, MD, USA
| | | | | | | | - Jill Joerger
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Laura L. Loftis
- Division of Critical Care Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Stephanie P. Schwartz
- Department of Pediatrics, University of North Carolina at Chapel Hill Children’s Hospital, Chapel Hill, NC, USA
| | - Tracie C. Walker
- Department of Pediatrics, University of North Carolina at Chapel Hill Children’s Hospital, Chapel Hill, NC, USA
| | - Julie C. Fitzgerald
- Division of Critical Care, Department of Anesthesiology and Critical Care, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Keiko M. Tarquinio
- Division of Critical Care Medicine, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Matt S. Zinter
- Department of Pediatrics, Divisions of Critical Care and Bone Marrow Transplantation, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer E. Schuster
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City MO, USA
| | - Natasha B. Halasa
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melissa L. Cullimore
- Department of Pediatrics, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Aline B. Maddux
- Department of Pediatrics, Section of Critical Care Medicine, University of Colorado School of Medicine and Children’s Hospital Colorado, Aurora, CO, USA
| | - Mary A. Staat
- Department of Pediatrics, University of Cincinnati, Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Katherine Irby
- Section of Pediatric Critical Care, Department of Pediatrics, Arkansas Children’s Hospital, Little Rock, AR, USA
| | - Heidi R. Flori
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Mott Children’s Hospital and University of Michigan, Ann Arbor, MI, USA
| | - Bria M. Coates
- Division of Critical Care Medicine, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Hillary Crandall
- Division of Pediatric Critical Care, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Shira J. Gertz
- Division of Pediatric Critical Care, Department of Pediatrics, Saint Barnabas Medical Center, Livingston, NJ, USA
| | - Adrienne G. Randolph
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital and Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| |
Collapse
|
27
|
Ke S, Pollock NR, Wang XW, Chen X, Daugherty K, Lin Q, Xu H, Garey KW, Gonzales-Luna AJ, Kelly CP, Liu YY. Integrating gut microbiome and host immune markers to understand the pathogenesis of Clostridioides difficile infection. Gut Microbes 2021; 13:1-18. [PMID: 34132169 PMCID: PMC8210874 DOI: 10.1080/19490976.2021.1935186] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile (C.difficile) infection is the most common cause of healthcare-associated infection and an important cause of morbidity and mortality among hospitalized patients. A comprehensive understanding of C.difficile infection (CDI) pathogenesis is crucial for disease diagnosis, treatment, and prevention. Here, we characterized gut microbial compositions and a broad panel of innate and adaptive immunological markers in 243 well-characterized human subjects (including 187 subjects with both microbiota and immune marker data), who were divided into four phenotype groups: CDI, Asymptomatic Carriage, Non-CDI Diarrhea, and Control. We found that the interactions between gut microbiota and host immune markers are very sensitive to the status of C.difficile colonization and infection. We demonstrated that incorporating both gut microbiome and host immune marker data into classification models can better distinguish CDI from other groups than can either type of data alone. Our classification models display robust diagnostic performance to differentiate CDI from Asymptomatic carriage (AUC~0.916), Non-CDI Diarrhea (AUC~0.917), or Non-CDI that combines all other three groups (AUC~0.929). Finally, we performed symbolic classification using selected features to derive simple mathematic formulas that explicitly quantify the interactions between the gut microbiome and host immune markers. These findings support the potential roles of gut microbiota and host immune markers in the pathogenesis of CDI. Our study provides new insights for a microbiome-immune marker-derived signature to diagnose CDI and design therapeutic strategies for CDI.
Collapse
Affiliation(s)
- Shanlin Ke
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MassachusettsUSA,School of Animal Science and Technology, State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University 330045, China
| | - Nira R. Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA,Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Xu-Wen Wang
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MassachusettsUSA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Qianyun Lin
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Kevin W. Garey
- Department of Pharmacy Practice and Translation Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Anne J. Gonzales-Luna
- Department of Pharmacy Practice and Translation Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Ciarán P. Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA,Ciarán P. Kelly Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MassachusettsUSA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MassachusettsUSA,CONTACT Yang-Yu Liu Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MassachusettsUSA
| |
Collapse
|
28
|
Schwenk HT, Pollock NR, Vaughan-Malloy AM. Pediatric Clostridioides difficile Infection: Diagnosis and Diagnostic Stewardship. J Pediatric Infect Dis Soc 2021; 10:S16-S21. [PMID: 34791395 DOI: 10.1093/jpids/piab054] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Although the pathogenesis of Clostridioides difficile infection (CDI) is complex and incompletely understood, it is believed that the elaboration of C. difficile toxins is necessary for disease. There are a variety of tests available for the detection of both the C. difficile organism and its toxins; however, each has limitations and the best application of these tests to the diagnosis of CDI in children remains uncertain. Nucleic acid amplification tests are unable to reliably discriminate between CDI and C. difficile colonization, while commercially available enzyme immunoassays for toxin detection lack sensitivity. An understanding of preanalytic factors, relevant patient features, and test performance characteristics is essential to the accurate diagnosis of CDI in children. Specific diagnostic stewardship strategies can also increase the likelihood that positive tests reflect disease rather than colonization. Ultimately, CDI remains a clinical diagnosis and clinical judgment is essential when interpreting test results, regardless of the methods used.
Collapse
Affiliation(s)
- Hayden T Schwenk
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Ana M Vaughan-Malloy
- Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
29
|
Branda JA, Lemieux JE, Blair L, Ahmed AA, Hong DK, Bercovici S, Blauwkamp TA, Hollemon D, Ho C, Strle K, Damle NS, Lepore TJ, Pollock NR. Detection of Borrelia burgdorferi Cell-free DNA in Human Plasma Samples for Improved Diagnosis of Early Lyme Borreliosis. Clin Infect Dis 2021; 73:e2355-e2361. [PMID: 32584965 PMCID: PMC8492203 DOI: 10.1093/cid/ciaa858] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 02/25/2020] [Accepted: 06/22/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Laboratory confirmation of early Lyme borreliosis (LB) is challenging. Serology is insensitive during the first days to weeks of infection, and blood polymerase chain reaction (PCR) offers similarly poor performance. Here, we demonstrate that detection of Borrelia burgdorferi (B.b.) cell-free DNA (cfDNA) in plasma can improve diagnosis of early LB. METHODS B.b. detection in plasma samples using unbiased metagenomic cfDNA sequencing performed by a commercial laboratory (Karius Inc) was compared with serology and blood PCR in 40 patients with physician-diagnosed erythema migrans (EM), 28 of whom were confirmed to have LB by skin biopsy culture (n = 18), seroconversion (n = 2), or both (n = 8). B.b. sequence analysis was performed using investigational detection thresholds, different from Karius' clinical test. RESULTS B.b. cfDNA was detected in 18 of 28 patients (64%) with laboratory-confirmed EM. In comparison, sensitivity of acute-phase serology using modified 2-tiered testing (MTTT) was 50% (P = .45); sensitivity of blood PCR was 7% (P = .0002). Combining B.b. cfDNA detection and MTTT increased diagnostic sensitivity to 86%, significantly higher than either approach alone (P ≤ .04). B.b. cfDNA sequences matched precisely with strain-specific sequence generated from the same individual's cultured B.b. isolate. B.b. cfDNA was not observed at any level in plasma from 684 asymptomatic ambulatory individuals. Among 3000 hospitalized patients tested as part of clinical care, B.b. cfDNA was detected in only 2 individuals, both of whom had clinical presentations consistent with LB. CONCLUSIONS This is the first report of B.b. cfDNA detection in early LB and a demonstration of potential diagnostic utility. The combination of B.b. cfDNA detection and acute-phase MTTT improves clinical sensitivity for diagnosis of early LB.
Collapse
Affiliation(s)
- John A Branda
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jacob E Lemieux
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Lily Blair
- Karius Inc, Redwood City, California, USA
| | | | | | | | | | | | - Carine Ho
- Karius Inc, Redwood City, California, USA
| | - Klemen Strle
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nitin S Damle
- South County Internal Medicine Inc, Wakefield, Rhode Island, USA
| | | | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
30
|
Alonso CD, Kelly CP, Garey KW, Gonzales-Luna AJ, Williams D, Daugherty K, Cuddemi C, Villafuerte-Gálvez J, White NC, Chen X, Xu H, Sprague R, Barrett C, Miller M, Foussadier A, Lantz A, Banz A, Pollock NR. Ultrasensitive and quantitative toxin measurement correlates with baseline severity, severe outcomes, and recurrence among hospitalized patients with Clostridioides difficile infection. Clin Infect Dis 2021; 74:2142-2149. [PMID: 34537841 DOI: 10.1093/cid/ciab826] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Stool toxin concentrations may impact Clostridioides difficile infection (CDI) severity and outcomes. We correlated fecal C. difficile toxin concentrations, measured by an ultrasensitive and quantitative assay, with CDI baseline severity, attributable outcomes, and recurrence. METHODS We enrolled 615 hospitalized adults (≥ 18y) with CDI (acute diarrhea, positive stool NAAT, and decision to treat). Baseline stool toxin A and B concentrations were measured by Single Molecule Array. Subjects were classified by baseline CDI severity (four scoring methods) and outcomes within 40 days (death, ICU stay, colectomy, and recurrence). RESULTS Among 615 patients (median 68.0 years), in all scoring systems, subjects with severe baseline disease had higher stool toxin A+B concentrations than those without (P<0.01). Nineteen subjects (3.1%) had a severe outcome primarily-attributed to CDI (group 1). This group had higher median toxin A+B [14,303 pg/mL (IQR 416.0, 141,967)] than subjects in whom CDI only contributed to the outcome [group 2, 163.2 pg/mL(0.0, 8423.3)], subjects with severe outcome unrelated to CDI [group 3, 158.6 pg/mL (0.0, 1795.2)], or no severe outcome [group 4, 209.5 pg/mL (0.0, 8566.3)](P=0.003). Group 1 was more likely to have detectable toxin (94.7%) than groups 2-4 (60.5-66.1%)(P=0.02). Individuals with recurrence had higher toxin A+B [2266.8 pg/mL(188.8, 29411)] than those without [154.0 pg/mL(0.0, 5864.3)](P<0.001) and higher rates of detectable toxin (85.7% versus 64.0%, P=0.004). CONCLUSIONS In CDI patients, ultrasensitive stool toxin detection and concentration correlated with severe baseline disease, severe CDI-attributable outcomes, and recurrence, confirming the contribution of toxin quantity to disease presentation and clinical course.
Collapse
Affiliation(s)
- Carolyn D Alonso
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Ciarán P Kelly
- Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College, of Pharmacy, Houston, TX, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College, of Pharmacy, Houston, TX, USA
| | - David Williams
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Christine Cuddemi
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Javier Villafuerte-Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nicole C White
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Rebecca Sprague
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Caitlin Barrett
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | | | | | - Nira R Pollock
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
31
|
Brümmer LE, Katzenschlager S, Gaeddert M, Erdmann C, Schmitz S, Bota M, Grilli M, Larmann J, Weigand MA, Pollock NR, Macé A, Carmona S, Ongarello S, Sacks JA, Denkinger CM. Accuracy of novel antigen rapid diagnostics for SARS-CoV-2: A living systematic review and meta-analysis. PLoS Med 2021; 18:e1003735. [PMID: 34383750 PMCID: PMC8389849 DOI: 10.1371/journal.pmed.1003735] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/26/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND SARS-CoV-2 antigen rapid diagnostic tests (Ag-RDTs) are increasingly being integrated in testing strategies around the world. Studies of the Ag-RDTs have shown variable performance. In this systematic review and meta-analysis, we assessed the clinical accuracy (sensitivity and specificity) of commercially available Ag-RDTs. METHODS AND FINDINGS We registered the review on PROSPERO (registration number: CRD42020225140). We systematically searched multiple databases (PubMed, Web of Science Core Collection, medRvix, bioRvix, and FIND) for publications evaluating the accuracy of Ag-RDTs for SARS-CoV-2 up until 30 April 2021. Descriptive analyses of all studies were performed, and when more than 4 studies were available, a random-effects meta-analysis was used to estimate pooled sensitivity and specificity in comparison to reverse transcription polymerase chain reaction (RT-PCR) testing. We assessed heterogeneity by subgroup analyses, and rated study quality and risk of bias using the QUADAS-2 assessment tool. From a total of 14,254 articles, we included 133 analytical and clinical studies resulting in 214 clinical accuracy datasets with 112,323 samples. Across all meta-analyzed samples, the pooled Ag-RDT sensitivity and specificity were 71.2% (95% CI 68.2% to 74.0%) and 98.9% (95% CI 98.6% to 99.1%), respectively. Sensitivity increased to 76.3% (95% CI 73.1% to 79.2%) if analysis was restricted to studies that followed the Ag-RDT manufacturers' instructions. LumiraDx showed the highest sensitivity, with 88.2% (95% CI 59.0% to 97.5%). Of instrument-free Ag-RDTs, Standard Q nasal performed best, with 80.2% sensitivity (95% CI 70.3% to 87.4%). Across all Ag-RDTs, sensitivity was markedly better on samples with lower RT-PCR cycle threshold (Ct) values, i.e., <20 (96.5%, 95% CI 92.6% to 98.4%) and <25 (95.8%, 95% CI 92.3% to 97.8%), in comparison to those with Ct ≥ 25 (50.7%, 95% CI 35.6% to 65.8%) and ≥30 (20.9%, 95% CI 12.5% to 32.8%). Testing in the first week from symptom onset resulted in substantially higher sensitivity (83.8%, 95% CI 76.3% to 89.2%) compared to testing after 1 week (61.5%, 95% CI 52.2% to 70.0%). The best Ag-RDT sensitivity was found with anterior nasal sampling (75.5%, 95% CI 70.4% to 79.9%), in comparison to other sample types (e.g., nasopharyngeal, 71.6%, 95% CI 68.1% to 74.9%), although CIs were overlapping. Concerns of bias were raised across all datasets, and financial support from the manufacturer was reported in 24.1% of datasets. Our analysis was limited by the included studies' heterogeneity in design and reporting. CONCLUSIONS In this study we found that Ag-RDTs detect the vast majority of SARS-CoV-2-infected persons within the first week of symptom onset and those with high viral load. Thus, they can have high utility for diagnostic purposes in the early phase of disease, making them a valuable tool to fight the spread of SARS-CoV-2. Standardization in conduct and reporting of clinical accuracy studies would improve comparability and use of data.
Collapse
Affiliation(s)
- Lukas E. Brümmer
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Mary Gaeddert
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Stephani Schmitz
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marc Bota
- Agaplesion Bethesda Hospital, Hamburg, Germany
| | - Maurizio Grilli
- Library, University Medical Center Mannheim, Mannheim, Germany
| | - Jan Larmann
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus A. Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | | | | | | | | | - Claudia M. Denkinger
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Partner Site Heidelberg University Hospital, German Center for Infection Research (DZIF), Heidelberg, Germany
| |
Collapse
|
32
|
Ciaranello A, Goehringer C, Nelson SB, Ruark LJ, Pollock NR. Lessons Learned From Implementation of SARS-CoV-2 Screening in K-12 Public Schools in Massachusetts. Open Forum Infect Dis 2021; 8:ofab287. [PMID: 34395706 PMCID: PMC8195145 DOI: 10.1093/ofid/ofab287] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/02/2021] [Indexed: 01/30/2023] Open
Abstract
In-person learning provides substantial benefits for K-12 school students. Risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among educators, staff, students, and household members can be markedly reduced by mitigation measures including masking, ventilation, and hygiene. In addition to these measures, where community transmission is moderate to high, regular SARS-CoV-2 screening testing is recommended by recent Centers for Disease Control and Prevention (CDC) guidance for unvaccinated K-12 students and staff, and supported financially by CDC and Department of Health and Human Services initiatives. Screening can provides an added layer of risk reduction, as well as data and reassurance about in-school transmission. Financial and logistical constraints have challenged implementation of screening in public schools. We report lessons learned from a collaborative of public K-12 schools implementing and evaluating screening programs, including details of population screened, site of specimen collection, assay selection, pooled testing, and resources needed. This work supported the development of a state-wide screening program and led to dissemination of online technical resources that may support other public schools in implementing CDC guidance.
Collapse
Affiliation(s)
- Andrea Ciaranello
- Division of Infectious Disease/Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Cathryn Goehringer
- COVID-19 Response Advisors, Washington, DC, USA
- Education Foundation, Wellesley, Massachusetts, USA
| | - Sandra B Nelson
- Division of Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Liz J Ruark
- COVID-19 Response Advisors, Washington, DC, USA
- Covidsafeschools.org, Harvard, Massachusetts, USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| |
Collapse
|
33
|
Pollock NR, Tran K, Jacobs JR, Cranston AE, Smith S, O’Kane CY, Roady TJ, Moran A, Scarry A, Carroll M, Volinsky L, Perez G, Patel P, Gabriel S, Lennon NJ, Madoff LC, Brown C, Smole SC. Performance and Operational Evaluation of the Access Bio CareStart Rapid Antigen Test in a High-Throughput Drive-Through Community Testing Site in Massachusetts. Open Forum Infect Dis 2021; 8:ofab243. [PMID: 34250188 PMCID: PMC8244626 DOI: 10.1093/ofid/ofab243] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/24/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND To facilitate deployment of point-of-care testing for severe acute respiratory syndrome coronavirus 2, we evaluated the Access Bio CareStart COVID-19 Antigen test in a high-throughput, drive-through, free community testing site using anterior nasal (AN) swab reverse-transcription polymerase chain reaction (RT-PCR) for clinical testing. METHODS Consenting symptomatic and asymptomatic children (≤18 years) and adults received dual AN swabs. CareStart testing was performed with temperature/humidity monitoring. All tests had 2 independent reads to assess interoperator agreement. Patients with positive CareStart results were called and instructed to isolate pending RT-PCR results. The paired RT-PCR result was the reference for sensitivity and specificity calculations. RESULTS Of 1603 participants, 1245 adults and 253 children had paired RT-PCR/CareStart results and complete symptom data. Eighty-three percent of adults and 87% of children were asymptomatic. CareStart sensitivity/specificity were 84.8% (95% confidence interval [CI], 71.1-93.7)/97.2% (95% CI, 92.0-99.4) and 85.7% (95% CI, 42.1-99.6)/89.5% (95% CI, 66.9-98.7) in adults and children, respectively, within 5 days of symptoms. Sensitivity/specificity were 50.0% (95% CI, 41.0-59.0)/99.1% (95% CI, 98.3-99.6) in asymptomatic adults and 51.4% (95% CI, 34.4-68.1)/97.8% (95% CI, 94.5-99.4) in asymptomatic children. Sensitivity in all 234 RT-PCR-positive people was 96.3% with cycle threshold (Ct) ≤25, 79.6% with Ct ≤30, and 61.4% with Ct ≤35. All 21 false-positive CareStart tests had faint but normal bands. Interoperator agreement was 99.5%. Operational challenges included identification of faint test bands and inconsistent swab elution volumes. CONCLUSIONS CareStart had high sensitivity in people with Ct ≤25 and moderate sensitivity in symptomatic people overall. Specificity was unexpectedly lower in symptomatic versus asymptomatic people. Excellent interoperator agreement was observed, but operational challenges indicate that operator training is warranted.
Collapse
Affiliation(s)
- Nira R Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Kristine Tran
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Jesica R Jacobs
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
- Laboratory Leadership Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amber E Cranston
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Sita Smith
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Claire Y O’Kane
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Tyler J Roady
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Anne Moran
- Lawrence General Hospital, Lawrence, Massachusetts, USA
| | - Alison Scarry
- Lawrence General Hospital, Lawrence, Massachusetts, USA
| | | | | | - Gloria Perez
- Lawrence General Hospital, Lawrence, Massachusetts, USA
| | - Pinal Patel
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Niall J Lennon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lawrence C Madoff
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
- Division of Infectious Disease and Immunology, Department of Medicine, University of Massachusetts Medical Center, Worcester, Massachusetts, USA
| | - Catherine Brown
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Sandra C Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| |
Collapse
|
34
|
Pollock NR, Lee F, Ginocchio CC, Yao JD, Humphries RM. Considerations for Assessment and Deployment of Rapid Antigen Tests for Diagnosis of Coronavirus Disease 2019. Open Forum Infect Dis 2021; 8:ofab110. [PMID: 34258309 PMCID: PMC7989197 DOI: 10.1093/ofid/ofab110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 11/16/2022] Open
Abstract
Diagnostic testing is a critical tool to mitigate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, but molecular testing capacity remains limited. Rapid diagnostic tests (RDTs) that detect SARS-CoV-2 protein antigens (Ag) offer the potential to substantially expand testing capacity and to allow frequent, large-scale, population screening. Testing is simple, rapid (results generally available within 15 minutes), and applicable for diagnosis at point of care. However, implementation of Ag RDTs requires a detailed understanding of test performance and operational characteristics in each testing scenario and population being evaluated. Successful implementation of Ag RDTs on a large scale should combine testing with technical oversight and with clinical and public health infrastructure, and will require production at levels much higher than presently possible. In this commentary, we provide detailed considerations for Ag RDT assessment and use cases to encourage and enable broader manufacturing and deployment.
Collapse
Affiliation(s)
- Nira R Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Francesca Lee
- Departments of Pathology and Internal Medicine, University of Texas, Southwestern Dallas, Texas, USA
| | | | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Romney M Humphries
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
35
|
Cao Y, Wang L, Ke S, Gálvez JAV, Pollock NR, Barret C, Sprague R, Daugherty K, Xu H, Lin Q, Yao J, Chen Y, Kelly CP, Liu YY, Chen X. Fecal Mycobiota Combined With Host Immune Factors Distinguish Clostridioides difficile Infection From Asymptomatic Carriage. Gastroenterology 2021; 160:2328-2339.e6. [PMID: 33684427 PMCID: PMC8169571 DOI: 10.1053/j.gastro.2021.02.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/16/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Although the role of gut microbiota in Clostridioides difficile infection (CDI) has been well established, little is known about the role of mycobiota in CDI. Here, we performed mycobiome data analysis in a well-characterized human cohort to evaluate the potential of using gut mycobiota features for CDI diagnosis. METHODS Stool samples were collected from 118 hospital patients, divided into 3 groups: CDI (n = 58), asymptomatic carriers (Carrier, n = 28), and Control (n = 32). The nuclear ribosomal DNA internal transcribed spacer 2 was sequenced using the Illumina HiSeq platform to assess the fungal composition. Downstream statistical analyses (including Alpha diversity analysis, ordination analysis, differential abundance analysis, fungal correlation network analysis, and classification analysis) were then performed. RESULTS Significant differences were observed in alpha and beta diversity between patients with CDI and Carrier (P < .05). Differential abundance analysis identified 2 genera (Cladosporium and Aspergillus) enriched in Carrier. The ratio of Ascomycota to Basidiomycota was dramatically higher in patients with CDI than in Carrier and Control (P < .05). Correlations between host immune factors and mycobiota features were weaker in patients with CDI than in Carrier. Using 4 fungal operational taxonomic units combined with 6 host immune markers in the random forest classifier can achieve very high performance (area under the curve ∼92.38%) in distinguishing patients with CDI from Carrier. CONCLUSIONS Our study provides specific markers of stool fungi combined with host immune factors to distinguish patients with CDI from Carrier. It highlights the importance of gut mycobiome in CDI, which may have been underestimated. Further studies on the diagnostic applications and therapeutic potentials of these findings are warranted.
Collapse
Affiliation(s)
- Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Lamei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Shanlin Ke
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Javier A. Villafuerte Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R. Pollock
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA,Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Caitlin Barret
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Rebecca Sprague
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Qianyun Lin
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Ciaran P. Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
| |
Collapse
|
36
|
Alonso CD, Papamichael K, Sprague R, Barrett C, Gonzales-Luna AJ, Daugherty K, Garey KW, Villafuerte-Gálvez J, Xu H, Lin Q, Wang L, Chen X, Pollock NR, Kelly CP. Humoral Immune Response to Clostridioides difficile Toxins A and B in Hospitalized Immunocompromised Patients With C difficile Infection. Open Forum Infect Dis 2021; 8:ofab286. [PMID: 34258317 PMCID: PMC8271131 DOI: 10.1093/ofid/ofab286] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/26/2021] [Indexed: 11/14/2022] Open
Abstract
Background The humoral immune response to Clostridioides difficile toxins in C difficile infection (CDI) is incompletely characterized in immunocompromised hosts (ICHs). Methods We conducted a prospective study of hospitalized adults with CDI, with and without immunosuppression (hematologic malignancy, active solid tumor, solid organ or stem cell transplant, inflammatory bowel disease, autoimmune disease, congenital or acquired immunodeficiency, asplenia, chronic receipt of high-dose steroids, or receipt of immunosuppressing medications within 12 months). Serum and stool antibody concentrations of immunoglobulin (Ig)M, IgG, and IgA to C difficile toxins A and B at treatment days 0, 3, and 10–14 were compared. Results Ninety-eight subjects (47 ICH; 51 non-ICH) were enrolled. Baseline serum antitoxin A and B antibody levels were similar. At day 3, ICHs demonstrated lower serum levels of antitoxin A IgG, antitoxin A IgA, and antitoxin B IgA (all P < .05). At day 10–14, lower antitoxin A IgG concentrations were observed in ICHs (ICH, 21 enzyme-linked immunosorbent assay [ELISA] units; interquartile range [IQR], 16.4–44.6) compared with non-ICH subjects (49.0 ELISA units; IQR, 21.5–103; P = .045). In stool, we observed lower concentrations of antitoxin B IgA antibodies at baseline and at day 3 for ICH subjects, with a notable difference in concentrations of antitoxin B IgA at day 3 (ICH, 6.7 ELISA units [IQR, 1.9–13.9] compared with non-ICH, 18.1 ELISA units [IQR, 4.9–31.7]; P = .003). Conclusions The ICHs with CDI demonstrated lower levels of C difficile antitoxin antibodies in serum and stool during early CDI therapy compared with non-ICHs. These data provide insight into the humoral response to CDI in ICHs.
Collapse
Affiliation(s)
- Carolyn D Alonso
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Konstantinos Papamichael
- Harvard Medical School, Boston, Massachusetts, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Rebecca Sprague
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Caitlin Barrett
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Javier Villafuerte-Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Qianyun Lin
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lamei Wang
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Nira R Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Ciarán P Kelly
- Harvard Medical School, Boston, Massachusetts, USA.,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| |
Collapse
|
37
|
Pollock NR, MacIntyre AT, Blauwkamp TA, Blair L, Ho C, Calderon R, Franke MF. Detection of Mycobacterium tuberculosis cell-free DNA to diagnose TB in pediatric and adult patients. Int J Tuberc Lung Dis 2021; 25:403-405. [PMID: 33977910 DOI: 10.5588/ijtld.21.0055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- N R Pollock
- Department of Laboratory Medicine, Boston Children´s Hospital and Harvard Medical School, Boston, MA
| | | | | | - L Blair
- Karius Inc, Redwood City, CA, USA
| | - C Ho
- Karius Inc, Redwood City, CA, USA
| | - R Calderon
- Socios En Salud Sucursal Peru, Lima, Peru, Programa Acadêmico de Tuberculose, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - M F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
38
|
Krüger LJ, Gaeddert M, Tobian F, Lainati F, Gottschalk C, Klein JAF, Schnitzler P, Kräusslich HG, Nikolai O, Lindner AK, Mockenhaupt FP, Seybold J, Corman VM, Drosten C, Pollock NR, Knorr B, Welker A, de Vos M, Sacks JA, Denkinger CM. The Abbott PanBio WHO emergency use listed, rapid, antigen-detecting point-of-care diagnostic test for SARS-CoV-2-Evaluation of the accuracy and ease-of-use. PLoS One 2021; 16:e0247918. [PMID: 34043631 PMCID: PMC8158996 DOI: 10.1371/journal.pone.0247918] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Diagnostics are essential for controlling the pandemic. Identifying a reliable and fast diagnostic device is needed for effective testing. We assessed performance and ease-of-use of the Abbott PanBio antigen-detecting rapid diagnostic test (Ag-RDT). METHODS This prospective, multi-centre diagnostic accuracy study enrolled at two sites in Germany. Following routine testing with reverse-transcriptase polymerase chain reaction (RT-PCR), a second study-exclusive swab was performed for Ag-RDT testing. Routine swabs were nasopharyngeal (NP) or combined NP/oropharyngeal (OP) whereas the study-exclusive swabs were NP. To evaluate performance, sensitivity and specificity were assessed overall and in predefined sub-analyses accordingly to cycle-threshold values, days after symptom onset, disease severity and study site. Additionally, an ease-of-use assessment (EoU) and System Usability Scale (SUS) were performed. RESULTS 1108 participants were enrolled between Sept 28 and Oct 30, 2020. Of these, 106 (9.6%) were PCR-positive. The Abbott PanBio detected 92/106 PCR-positive participants with a sensitivity of 86.8% (95% CI: 79.0% - 92.0%) and a specificity of 99.9% (95% CI: 99.4%-100%). The sub-analyses indicated that sensitivity was 95.8% in Ct-values <25 and within the first seven days from symptom onset. The test was characterized as easy to use (SUS: 86/100) and considered suitable for point-of-care settings. CONCLUSION The Abbott PanBio Ag-RDT performs well for SARS-CoV-2 testing in this large manufacturer independent study, confirming its WHO recommendation for Emergency Use in settings with limited resources.
Collapse
Affiliation(s)
- Lisa J Krüger
- Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Mary Gaeddert
- Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Tobian
- Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Federica Lainati
- Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Claudius Gottschalk
- Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Julian A F Klein
- Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Paul Schnitzler
- Virology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Olga Nikolai
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Andreas K Lindner
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Frank P Mockenhaupt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Joachim Seybold
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Directorate, Berlin, Germany
| | - Victor M Corman
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), Partner Site Charité, Berlin, Germany
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), Partner Site Charité, Berlin, Germany
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, United States of America
| | - Britta Knorr
- Department of Public Health Rhein Neckar Region, Heidelberg, Germany
| | - Andreas Welker
- Department of Public Health Rhein Neckar Region, Heidelberg, Germany
| | | | - Jilian A Sacks
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Claudia M Denkinger
- Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
- German Centre for Infection Research (DZIF), Partner Site Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
39
|
Lee RA, Herigon JC, Benedetti A, Pollock NR, Denkinger CM. Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:JCM.02881-20. [PMID: 33504593 DOI: 10.1101/2020.11.12.20230748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Indexed: 05/23/2023] Open
Abstract
Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.
Collapse
Affiliation(s)
- Rose A Lee
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Joshua C Herigon
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Benedetti
- Department of Medicine and of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Nira R Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Claudia M Denkinger
- Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
40
|
Pollock NR, Jacobs JR, Tran K, Cranston AE, Smith S, O'Kane CY, Roady TJ, Moran A, Scarry A, Carroll M, Volinsky L, Perez G, Patel P, Gabriel S, Lennon NJ, Madoff LC, Brown C, Smole SC. Performance and Implementation Evaluation of the Abbott BinaxNOW Rapid Antigen Test in a High-Throughput Drive-Through Community Testing Site in Massachusetts. J Clin Microbiol 2021; 59:e00083-21. [PMID: 33622768 PMCID: PMC8091851 DOI: 10.1128/jcm.00083-21] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [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: 01/12/2021] [Accepted: 02/19/2021] [Indexed: 11/20/2022] Open
Abstract
Rapid diagnostic tests (RDTs) for SARS-CoV-2 antigens (Ag) that can be performed at point of care (POC) can supplement molecular testing and help mitigate the COVID-19 pandemic. Deployment of an Ag RDT requires an understanding of its operational and performance characteristics under real-world conditions and in relevant subpopulations. We evaluated the Abbott BinaxNOW COVID-19 Ag card in a high-throughput, drive-through, free community testing site in Massachusetts using anterior nasal (AN) swab reverse transcriptase PCR (RT-PCR) for clinical testing. Individuals presenting for molecular testing in two of seven lanes were offered the opportunity to also receive BinaxNOW testing. Dual AN swabs were collected from symptomatic and asymptomatic children (≤18 years of age) and adults. BinaxNOW testing was performed in a testing pod with temperature/humidity monitoring. One individual performed testing and official result reporting for each test, but most tests had a second independent reading to assess interoperator agreement. Positive BinaxNOW results were scored as faint, medium, or strong. Positive BinaxNOW results were reported to patients by phone, and they were instructed to isolate pending RT-PCR results. The paired RT-PCR result was the reference for sensitivity and specificity calculations. Of 2,482 participants, 1,380 adults and 928 children had paired RT-PCR/BinaxNOW results and complete symptom data. In this study, 974/1,380 (71%) adults and 829/928 (89%) children were asymptomatic. BinaxNOW had 96.5% (95% confidence interval [CI], 90.0 to 99.3) sensitivity and 100% (95% CI, 98.6 to 100.0) specificity in adults within 7 days of symptoms and 84.6% (95% CI, 65.1 to 95.6) sensitivity and 100% (95% CI, 94.5 to 100.0) specificity in children within 7 days of symptoms. Sensitivity and specificity in asymptomatic adults were 70.2% (95% CI, 56.6 to 81.6) and 99.6% (95% CI, 98.9 to 99.9), respectively, and in asymptomatic children, they were 65.4% (95% CI, 55.6 to 74.4) and 99.0% (95% CI, 98.0 to 99.6), respectively. By cycle threshold (CT ) value cutoff, sensitivity in all subgroups combined (n = 292 RT-PCR-positive individuals) was 99.3% with CT values of ≤25, 95.8% with CT values of ≤30, and 81.2% with CT values of ≤35. Twelve false-positive BinaxNOW results (out of 2,308 tests) were observed; in all 12, the test bands were faint but otherwise normal and were noted by both readers. One invalid BinaxNOW result was identified. Interoperator agreement (positive versus negative BinaxNOW result) was 100% (n = 2,230/2,230 double reads). Each operator was able to process 20 RDTs per hour. In a separate set of 30 specimens (from individuals with symptoms ≤7 days) run at temperatures below the manufacturer's recommended range (46 to 58.5°F), sensitivity was 66.7% and specificity 95.2%. BinaxNOW had very high specificity in both adults and children and very high sensitivity in newly symptomatic adults. Overall, 95.8% sensitivity was observed with CT values of ≤30. These data support public health recommendations for use of the BinaxNOW test in adults with symptoms for ≤7 days without RT-PCR confirmation. Excellent interoperator agreement indicates that an individual can perform and read the BinaxNOW test alone. A skilled laboratorian can perform and read 20 tests per hour. Careful attention to temperature is critical.
Collapse
Affiliation(s)
- Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jesica R Jacobs
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
- Laboratory Leadership Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kristine Tran
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Amber E Cranston
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Sita Smith
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Claire Y O'Kane
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Tyler J Roady
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Anne Moran
- Lawrence General Hospital, Lawrence, Massachusetts, USA
| | - Alison Scarry
- Lawrence General Hospital, Lawrence, Massachusetts, USA
| | | | | | - Gloria Perez
- Lawrence General Hospital, Lawrence, Massachusetts, USA
| | - Pinal Patel
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Niall J Lennon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lawrence C Madoff
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
- Division of Infectious Disease and Immunology, Department of Medicine, University of Massachusetts Medical Center, Worcester, Massachusetts, USA
| | - Catherine Brown
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Sandra C Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| |
Collapse
|
41
|
Lee RA, Herigon JC, Benedetti A, Pollock NR, Denkinger CM. Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:e02881-20. [PMID: 33504593 PMCID: PMC8091856 DOI: 10.1128/jcm.02881-20] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.
Collapse
Affiliation(s)
- Rose A Lee
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Joshua C Herigon
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Benedetti
- Department of Medicine and of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Nira R Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Claudia M Denkinger
- Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
42
|
Pollock NR, Savage TJ, Wardell H, Lee RA, Mathew A, Stengelin M, Sigal GB. Correlation of SARS-CoV-2 Nucleocapsid Antigen and RNA Concentrations in Nasopharyngeal Samples from Children and Adults Using an Ultrasensitive and Quantitative Antigen Assay. J Clin Microbiol 2021; 59:e03077-20. [PMID: 33441395 PMCID: PMC8092747 DOI: 10.1128/jcm.03077-20] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/11/2021] [Indexed: 01/14/2023] Open
Abstract
Diagnosis of COVID-19 by PCR offers high sensitivity, but the utility of detecting samples with high cycle threshold (CT ) values remains controversial. Currently available rapid diagnostic tests (RDTs) for SARS-CoV-2 nucleocapsid antigens (Ag) have sensitivity well below PCR. The correlation of Ag and RNA quantities in clinical nasopharyngeal (NP) samples is unknown. An ultrasensitive, quantitative electrochemiluminescence immunoassay for SARS-CoV-2 nucleocapsid (the MSD S-PLEX SARS-CoV-2 N assay) was used to measure Ag in clinical NP samples from adults and children previously tested by PCR. The S-PLEX Ag assay had a limit of detection (LOD) of 0.16 pg/ml and a cutoff of 0.32 pg/ml. Ag concentrations measured in clinical NP samples (collected in 3.0 ml of media) ranged from less than 160 fg/ml to 2.7 μg/ml. Log-transformed Ag concentrations correlated tightly with CT values. In 35 adult and 101 pediatric PCR-positive samples, the sensitivities were 91% (95% confidence interval, 77 to 98%) and 79% (70 to 87%), respectively. In samples with a CT of ≤35, the sensitivities were 100% (88 to 100%) and 96% (88 to 99%), respectively. In 50 adult and 40 pediatric PCR-negative specimens, the specificities were 100% (93 to 100%) and 98% (87 to 100%), respectively. Nucleocapsid concentrations in clinical NP samples span 8 orders of magnitude and correlate closely with RNA concentrations (CT values). The S-PLEX Ag assay showed 96 to 100% sensitivity in samples from children and adults with CT values of ≤35, and a specificity of 98 to 100%. These results clarify Ag concentration distributions in clinical samples, providing insight into the performance of Ag RDTs and offering a new approach to diagnosis of COVID-19.
Collapse
Affiliation(s)
- Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Timothy J Savage
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Hanna Wardell
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Rose A Lee
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Anu Mathew
- Meso Scale Diagnostics, LLC., Rockville, Maryland, USA
| | | | | |
Collapse
|
43
|
Humphries RM, Azar MM, Caliendo AM, Chou A, Colgrove RC, Fabre V, Ginocchio CC, Hanson KE, Hayden MK, Pillai DR, Pollock NR, Lee FM. To Test, Perchance to Diagnose: Practical Strategies for Severe Acute Respiratory Syndrome Coronavirus 2 Testing. Open Forum Infect Dis 2021; 8:ofab095. [PMID: 33880392 PMCID: PMC7989172 DOI: 10.1093/ofid/ofab095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 01/08/2023] Open
Abstract
Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in symptomatic and asymptomatic patients is an important component of the multifaceted approach of managing the coronavirus disease 2019 pandemic. Determining how to best define testing strategies for different populations and incorporating these into broader infection prevention programs can be complex. Many circumstances are not addressed by federal, local, or professional guidelines. This commentary describes various scenarios in which testing of symptomatic or asymptomatic individuals for SARS-CoV-2 virus (antigen or ribonucleic acid) can be of potential benefit. Consideration to pretest probability, risks of testing (impact of false-positive or false-negative results), testing strategy, as well as action based on test results are explored. Testing, regardless of setting, must be incorporated into overarching infection control plans, which include use of personal protective equipment (eg, masks), physically distancing, and isolation when exposure is suspected.
Collapse
Affiliation(s)
| | - Marwan M Azar
- Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Angela M Caliendo
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Andrew Chou
- Michael E. DeBakey VA Medical Center, Baylor College of Medicine, Houston, Texas, USA
| | - Robert C Colgrove
- Division of Infectious Diseases, Mount Auburn Hospital, Harvard School of Medicine, Boston, Massachusetts, USA
| | - Valeria Fabre
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Kimberly E Hanson
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Section of Clinical Microbiology, Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA.,Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Dylan R Pillai
- Departments of Pathology, Medicine, and Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Francesca M Lee
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
44
|
Lin Q, Pollock NR, Banz A, Lantz A, Xu H, Gu L, Gerding DN, Garey KW, Gonzales-Luna AJ, Zhao M, Song L, Duffy DC, Kelly CP, Chen X. Toxin A-Predominant Pathogenic Clostridioides difficile: A Novel Clinical Phenotype. Clin Infect Dis 2021; 70:2628-2633. [PMID: 31400280 DOI: 10.1093/cid/ciz727] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Most Clostridioides difficile toxinogenic strains produce both toxins A and B (A+B+), but toxin A-negative, toxin B-positive (A-B+) variants also cause disease. We report the identification of a series of pathogenic clinical C. difficile isolates that produce high amounts of toxin A with low or nondetectable toxin B. METHODS An ultrasensitive, quantitative immunoassay was used to measure toxins A and B in stool samples from 187 C. difficile infection (CDI) patients and 44 carriers. Isolates were cultured and assessed for in vitro toxin production and in vivo phenotypes (mouse CDI model). RESULTS There were 7 CDI patients and 6 carriers who had stools with detectable toxin A (TcdA, range 23-17 422 pg/mL; 5.6% of samples overall) but toxin B (TcdB) below the clinical detection limit (<20 pg/mL; median TcdA:B ratio 17.93). Concentrations of toxin A far exceeded B in in vitro cultures of all 12 recovered isolates (median TcdA:B ratio 26). Of 8 toxin A>>B isolates tested in mice, 4 caused diarrhea, and 3 of those 4 caused lethal disease. Ribotyping demonstrated strain diversity. TcdA-predominant samples were also identified at 2 other centers, with similar frequencies (7.5% and 6.8%). CONCLUSIONS We report the discovery of clinical pathogenic C. difficile strains that produce high levels of toxin A but minimal or no toxin B. This pattern of toxin production is not rare (>5% of isolates) and is consistently observed in vitro and in vivo in humans and mice. Our study highlights the significance of toxin A in human CDI pathogenesis and has important implications for CDI diagnosis, treatment, and vaccine development.
Collapse
Affiliation(s)
- Qianyun Lin
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Divisions of Gastroenterology, Massachusetts
| | - Nira R Pollock
- Infectious Diseases, Beth Israel Deaconess Medical Center, Massachusetts.,Department of Laboratory Medicine, Boston Children's Hospital, Massachusetts
| | | | | | - Hua Xu
- Divisions of Gastroenterology, Massachusetts
| | - Limei Gu
- Divisions of Gastroenterology, Massachusetts
| | - Dale N Gerding
- Department of Veterans Affairs, Edward Hines Jr Veterans Affairs Hospital, Hines, Illinois
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | | | | | | | | | - Xinhua Chen
- Divisions of Gastroenterology, Massachusetts
| |
Collapse
|
45
|
Kelly CP, Chen X, Williams D, Xu H, Cuddemi CA, Daugherty K, Barrett C, Miller M, Foussadier A, Lantz A, Banz A, Pollock NR. Host Immune Markers Distinguish Clostridioides difficile Infection From Asymptomatic Carriage and Non-C. difficile Diarrhea. Clin Infect Dis 2021; 70:1083-1093. [PMID: 31211839 DOI: 10.1093/cid/ciz330] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/22/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Recent data indicate that Clostridioides difficile toxin concentrations in stool do not differentiate between C. difficile infection (CDI) and asymptomatic carriage. Thus, we lack a method to distinguish a symptomatic patient with CDI from a colonized patient with diarrhea from another cause. To address this, we evaluated markers of innate and adaptive immunity in adult inpatients with CDI (diagnosed per US guidelines), asymptomatic carriage, or non-CDI diarrhea. METHODS CDI-NAAT patients had clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment. Carrier-NAAT patients had positive stool NAAT but no diarrhea. NAAT-negative patients (with and without diarrhea) were also enrolled. A panel of cytokines and anti-toxin A and B immunoglobulin (Ig) were measured in serum; calprotectin and anti-toxin B Ig A/G were measured in stool. NAAT-positive stool samples were tested by an ultrasensitive toxin assay (clinical cutoff, 20 pg/mL). RESULTS Median values for interleukin (IL)-4, IL-6, IL-8, IL-10, IL-15, granulocyte colony-stimulating factor (GCSF), MCP-1, tumor necrosis factor α (TNF-α), and IgG anti-toxin A in blood and IgA/G anti-toxin B in stool were significantly higher in CDI patients compared with all other groups (P < .05). Concentration distributions for IL-6, GCSF, TNF-α, and IgG anti-toxin A in blood, as well as IgA and IgG anti-toxin B in stool, separated CDI patients from all other groups. CONCLUSIONS Specific markers of innate and adaptive immunity distinguish CDI from all other groups, suggesting potential clinical utility for identifying which NAAT- and toxin-positive patients with diarrhea truly have CDI.
Collapse
Affiliation(s)
- Ciaran P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Massachusetts
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Massachusetts
| | - David Williams
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Massachusetts
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Massachusetts
| | - Christine A Cuddemi
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Massachusetts
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Massachusetts
| | - Caitlin Barrett
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Massachusetts
| | | | | | | | | | - Nira R Pollock
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center.,Department of Laboratory Medicine, Boston Children's Hospital, Massachusetts
| |
Collapse
|
46
|
Rosenbohm JM, Robson JM, Singh R, Lee R, Zhang JY, Klapperich CM, Pollock NR, Cabodi M. Rapid electrostatic DNA enrichment for sensitive detection of Trichomonas vaginalis in clinical urinary samples. Anal Methods 2020; 12:1085-1093. [PMID: 35154421 PMCID: PMC8837197 DOI: 10.1039/c9ay02478f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Estimated to be the most common non-viral sexually transmitted infection globally, Trichomonas vaginalis (TV) can lead to pelvic inflammatory disease, pregnancy complications, and increased risk of acquiring and transmitting HIV. Once diagnosed, TV infection can be treated with oral antibiotics; however, infected individuals are often asymptomatic and do not seek treatment. The WHO and others have identified a need for point-of-care tests to expand access to TV testing and screening; ideal test characteristics include high sensitivity and specificity and the ability to use urine as a sample type, rather than invasively collected swab samples. Here, we report on a proof-of-concept prototype for rapid, electrostatic enrichment of DNA from urine samples and demonstrate the use of large volumes of urine to increase sensitivity of downstream nucleic acid amplification testing. We developed an internally controlled thermophilic helicase-dependent amplification (tHDA) assay with lateral flow immunoassay readout and demonstrate that this tHDA assay can be performed directly on our DNA capture filter. We validated our method using clinical urine samples with qPCR-quantified TV loads. Using 62 clinical urine samples and a simple sample processing device, our tHDA assay displayed 96.6% sensitivity and 100% specificity. Our analytical limit of detection was found to be approximately 7 genomic equivalents of TV DNA per mL of sample when 1 mL of sample was tested, comparable to existing isothermal tests for TV. Using large-volume simulated samples (40 mL of buffered urine with spiked-in TV DNA), we also demonstrated that sensitivity could be improved 28-fold to 0.25 genomic equivalents of TV DNA per mL, with a sample processing time of only 2 minutes.
Collapse
Affiliation(s)
| | - James M. Robson
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Rishabh Singh
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Rose Lee
- Department of Laboratory Medicine (NRP) and Division of Infectious Diseases (RL), Boston Children’s Hospital, Boston, MA, USA
| | - Jane Y. Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | | | - Nira R. Pollock
- Department of Laboratory Medicine (NRP) and Division of Infectious Diseases (RL), Boston Children’s Hospital, Boston, MA, USA
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| |
Collapse
|
47
|
Pollock NR, Banz A, Chen X, Williams D, Xu H, Cuddemi CA, Cui AX, Perrotta M, Alhassan E, Riou B, Lantz A, Miller MA, Kelly CP. Comparison of Clostridioides difficile Stool Toxin Concentrations in Adults With Symptomatic Infection and Asymptomatic Carriage Using an Ultrasensitive Quantitative Immunoassay. Clin Infect Dis 2020; 68:78-86. [PMID: 29788296 DOI: 10.1093/cid/ciy415] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
Background We used an ultrasensitive, quantitative single molecule array (Simoa) immunoassay to test whether concentrations of Clostridioides (formerly Clostridium) difficile toxins A and/or B in the stool of adult inpatients with C. difficile infection (CDI) were higher than in asymptomatic carriers of toxinogenic C. difficile. Methods Patients enrolled as CDI-NAAT had clinically significant diarrhea and a positive nucleic acid amplification test (NAAT), per US guidelines, and received CDI treatment. Potential carriers had recently received antibiotics and did not have diarrhea; positive NAAT confirmed carriage. Baseline stool samples were tested by Simoa for toxin A and B. Results Stool toxin concentrations in both CDI-NAAT (n = 122) and carrier-NAAT (n = 44) cohorts spanned 5 logs (0 pg/mL to >100000 pg/mL). Seventy-nine of 122 (65%) CDI-NAAT and 34 of 44 (77%) carrier-NAAT had toxin A + B concentration ≥20 pg/mL (clinical cutoff). Median toxin A, toxin B, toxin A + B, and NAAT cycle threshold (Ct) values in CDI-NAAT and carrier-NAAT cohorts were similar (toxin A, 50.6 vs 60.0 pg/mL, P = .958; toxin B, 89.5 vs 42.3 pg/mL, P = .788; toxin A + B, 197.2 vs 137.3 pg/mL, P = .766; Ct, 28.1 vs 28.6, P = .354). However, when CDI/carrier cohorts were limited to those with detectable toxin, respective medians were significantly different (A: 874.0 vs 129.7, P = .021; B: 1317.0 vs 81.7, P = .003, A + B, 4180.7 vs 349.6, P = .004; Ct, 25.8 vs 27.7, P = .015). Conclusions Toxin concentration did not differentiate an individual with CDI from one with asymptomatic carriage. Median stool toxin concentrations in groups with CDI vs carriage differed, but only when groups were defined by detectable stool toxin (vs positive NAAT).
Collapse
Affiliation(s)
- Nira R Pollock
- Divisions of Infectious Disease and Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston.,Department of Laboratory Medicine, Boston Children's Hospital, Massachusetts
| | | | - Xinhua Chen
- Divisions of Infectious Disease and Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston
| | - David Williams
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Massachusetts
| | - Hua Xu
- Divisions of Infectious Disease and Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston
| | - Christine A Cuddemi
- Divisions of Infectious Disease and Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston
| | - Alice X Cui
- Divisions of Infectious Disease and Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston
| | - Matthew Perrotta
- Divisions of Infectious Disease and Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston
| | - Eaman Alhassan
- Divisions of Infectious Disease and Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston
| | | | | | | | - Ciaran P Kelly
- Divisions of Infectious Disease and Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston
| |
Collapse
|
48
|
Bulterys MA, Wagner B, Redard-Jacot M, Suresh A, Pollock NR, Moreau E, Denkinger CM, Drain PK, Broger T. Point-Of-Care Urine LAM Tests for Tuberculosis Diagnosis: A Status Update. J Clin Med 2019; 9:E111. [PMID: 31906163 PMCID: PMC7020089 DOI: 10.3390/jcm9010111] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022] Open
Abstract
Most diagnostic tests for tuberculosis (TB) rely on sputum samples, which are difficult to obtain and have low sensitivity in immunocompromised patients, patients with disseminated TB, and children, delaying treatment initiation. The World Health Organization (WHO) calls for the development of a rapid, biomarker-based, non-sputum test capable of detecting all forms of TB at the point-of-care to enable immediate treatment initiation. Lipoarabinomannan (LAM) is the only WHO-endorsed TB biomarker that can be detected in urine, an easily collected sample. This status update discusses the characteristics of LAM as a biomarker, describes the performance of first-generation urine LAM tests and reasons for slow uptake, and presents considerations for developing the next generation of more sensitive and impactful tests. Next-generation urine LAM tests have the potential to reach adult and pediatric patients regardless of HIV status or site of infection and facilitate global TB control. Implementation and scale-up of existing LAM tests and development of next-generation assays should be prioritized.
Collapse
Affiliation(s)
- Michelle A. Bulterys
- FIND, 1202 Geneva, Switzerland
- International Clinical Research Center, University of Washington, Seattle, WA 98105, USA
| | | | | | | | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | | | - Claudia M. Denkinger
- FIND, 1202 Geneva, Switzerland
- Division of Tropical Medicine, Center of Infectious Diseases, University of Heidelberg, 69120 Heidelberg, Germany
| | - Paul K. Drain
- International Clinical Research Center, University of Washington, Seattle, WA 98105, USA
| | | |
Collapse
|
49
|
Brock M, Hanlon D, Zhao M, Pollock NR. Detection of mycobacterial lipoarabinomannan in serum for diagnosis of active tuberculosis. Diagn Microbiol Infect Dis 2019; 96:114937. [PMID: 31785971 DOI: 10.1016/j.diagmicrobio.2019.114937] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023]
Abstract
Urinary detection of Mycobacterium tuberculosis lipoarabinomannan (LAM) for tuberculosis (TB) diagnosis is well characterized, but the utility of serum LAM detection remains unclear. We developed an assay for serum LAM detection using single-molecule array (Simoa), purified M. tuberculosis LAM, and anti-LAM monoclonal antibodies and evaluated performance on diluted/heat-treated serum samples from patients with and without active TB and/or HIV. The Simoa assay had a limit of detection of 0.35 pg/mL and lower limit of quantification of 0.942 pg/mL. Corrected serum LAM concentrations ranged from 0 to 132.0 pg/mL [median 1.71, interquartile range (IQR) 0.94-6.80] in 90 TB+ patients and from 0 to 2.29 pg/mL (median 1.03, IQR 0.47-1.69) in 55 TB- patients. Using a cutoff of 2.3 pg/mL for 100% specificity, assay sensitivity was 37% in all TB+ subjects (33/90; 95% CI 0.27-0.48), 47% in TB+/HIV+ subjects (26/55; 0.34-0.61), and 60% in TB+/HIV+/smear+ subjects (21/35; 0.42-0.76). Mycobacterial LAM is detectable in serum with high specificity and reasonable sensitivity using Simoa.
Collapse
Affiliation(s)
| | | | | | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA.
| |
Collapse
|
50
|
Mesman AW, Soto M, Coit J, Calderon R, Aliaga J, Pollock NR, Mendoza M, Mestanza FM, Mendoza CJ, Murray MB, Lecca L, Holmberg R, Franke MF. Correction to: Detection of Mycobacterium tuberculosis in pediatric stool samples using TruTip technology. BMC Infect Dis 2019; 19:856. [PMID: 31619179 PMCID: PMC6796466 DOI: 10.1186/s12879-019-4483-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Annelies W Mesman
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA
| | - Martin Soto
- Socios En Salud Sucursal (Partners In Health), Lima, Peru
| | - Julia Coit
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA
| | - Roger Calderon
- Socios En Salud Sucursal (Partners In Health), Lima, Peru
| | - Juan Aliaga
- Socios En Salud Sucursal (Partners In Health), Lima, Peru
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, USA
| | | | | | | | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA
| | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA.,Socios En Salud Sucursal (Partners In Health), Lima, Peru
| | | | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA.
| |
Collapse
|