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Gill CJ, Gunning CE, MacLeod WB, Mwananyanda L, Thea DM, Pieciak RC, Kwenda G, Mupila Z, Rohani P. Asymptomatic Bordetella pertussis infections in a longitudinal cohort of young African infants and their mothers. eLife 2021; 10:65663. [PMID: 34097599 PMCID: PMC8184211 DOI: 10.7554/elife.65663] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/26/2021] [Indexed: 12/17/2022] Open
Abstract
Recent pertussis resurgence in numerous countries may be driven by asymptomatic infections. Most pertussis surveillance studies are cross-sectional and cannot distinguish asymptomatic from pre-symptomatic infections. Longitudinal surveillance could overcome this barrier, providing more information about the true burden of pertussis at the population level. Here we analyze 17,442 nasopharyngeal samples from a longitudinal cohort of 1320 Zambian mother/infant pairs. Our analysis has two elements. First, we demonstrate that the full range of IS481 qPCR CT values provides insight into pertussis epidemiology, showing concordance of low and high CT results over time, within mother/infant pairs, and in relation to symptomatology. Second, we exploit these full-range qPCR data to demonstrate a high incidence of asymptomatic pertussis, including among infants. Our results demonstrate a wider burden of pertussis infection than we anticipated in this population, and expose key limitations of threshold-based interpretation of qPCR results in infectious disease surveillance.
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Affiliation(s)
- Christopher J Gill
- Boston University School of Public Health, Department of Global Health, Boston, United States
| | | | - William B MacLeod
- Boston University School of Public Health, Department of Global Health, Boston, United States
| | - Lawrence Mwananyanda
- Boston University School of Public Health, Department of Global Health, Boston, United States.,Right to Care, Lusaka, Zambia
| | - Donald M Thea
- Boston University School of Public Health, Department of Global Health, Boston, United States
| | - Rachel C Pieciak
- Boston University School of Public Health, Department of Global Health, Boston, United States
| | - Geoffrey Kwenda
- University of Zambia, School of Health Sciences, Department of Biomedical Science, Lusaka, Zambia
| | | | - Pejman Rohani
- University of Georgia, Odum School of Ecology, Athens, Georgia.,University of Georgia, Center for the Ecology of Infectious Diseases, Athens, Georgia.,University of Georgia, Department of Infectious Diseases, Athens, Georgia
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Gill CJ, Gunning CE, MacLeod W, Mwananyanda L, Thea D, Pieciak R, Kwenda G, Mupila Z, Rohani P. Asymptomatic Bordetella pertussis infections in young African infants and their mothers identified within a longitudinal cohort. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.11.18.20231423. [PMID: 33236026 PMCID: PMC7685339 DOI: 10.1101/2020.11.18.20231423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Despite long-standing vaccination programs, pertussis incidence has increased in numerous countries; transmission by asymptomatic individuals is a suspected driver of this resurgence. However, unequivocal evidence documenting asymptomatic infections in adults and children is lacking due, in part, to the cross-sectional nature of most pertussis surveillance studies. In addition, modern pertussis surveillance relies on quantitative PCR (qPCR) using fixed diagnostic thresholds to identify cases. To address this gap, we present a longitudinal analysis of 17,442 nasopharyngeal samples collected from a cohort of 1,320 Zambian mother/infant pairs. Using full-range cycle threshold (CT) values from IS481 qPCR assays, we document widespread asymptomatic infections among mothers and also, surprisingly, among young infants. From an initial group of eight symptomatic infants who tested positive by qPCR, we identify frequent contemporaneous subclinical infections in mothers. Within the full cohort, we observe strong temporal correlation between low- and high-intensity qPCR signals. We compute a single time-averaged score for each individual summarizing the evidence for pertussis infection (EFI), and show that EFI strongly clusters within mother/infant pairs, and is strongly associated with clinical symptomatology and antibiotic use. Overall, the burden of pertussis here is substantially underestimated when restricting diagnostic criteria to IS481 CT≤35. Rather, we find that full-range CT values provide valuable insights into pertussis epidemiology in this population, and illuminate the infection arc within individuals. These findings have significant implications for quantifying asymptomatic pertussis prevalence and its contribution to overall transmission. Our results also expose limitations of threshold-based interpretations of qPCR assays in infectious disease surveillance.
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Affiliation(s)
- C J Gill
- Boston University School of Public Health, Deptartment of Global Health
| | - C E Gunning
- University of Georgia, Odum School of Ecology
| | - W MacLeod
- Boston University School of Public Health, Deptartment of Global Health
| | - L Mwananyanda
- Boston University School of Public Health, Deptartment of Global Health
- Right to Care - Zambia
| | - D Thea
- Boston University School of Public Health, Deptartment of Global Health
| | - R Pieciak
- Boston University School of Public Health, Deptartment of Global Health
| | - G Kwenda
- University of Zambia, School of Health Sciences, Department of Biomedical Science
| | | | - P Rohani
- University of Georgia, Odum School of Ecology
- University of Georgia, Center for the Ecology of Infectious Diseases
- University of Georgia, Department of Infectious Diseases
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Sung H, Roh KH, Hong KH, Seong MW, Ryoo N, Kim HS, Lee J, Kim SY, Ryu SW, Kim MN, Han MG, Lee SW, Lee H, Yoo CK. COVID-19 Molecular Testing in Korea: Practical Essentials and Answers From Experts Based on Experiences of Emergency Use Authorization Assays. Ann Lab Med 2020; 40:439-447. [PMID: 32539299 PMCID: PMC7295959 DOI: 10.3343/alm.2020.40.6.439] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/28/2020] [Accepted: 05/29/2020] [Indexed: 01/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Early detection of COVID-19 and immediate isolation of infected patients from the naive population are important to prevent further pandemic spread of the infection. Real-time reverse transcription (RT)-PCR to detect SARS-CoV-2 RNA is currently the most reliable diagnostic method for confirming COVID-19 worldwide. Guidelines for clinical laboratories on the COVID-19 diagnosis have been recently published by Korean Society for Laboratory Medicine and the Korea Centers for Disease Control and Prevention. However, these formal guidelines do not address common practical laboratory issues related to COVID-19 real-time RT-PCR testing and their solutions. Therefore, this guideline is intended as a practical and technical supplement to the “Guidelines for Laboratory Diagnosis of COVID-19 in Korea”.
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Affiliation(s)
- Heungsup Sung
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Kyoung Ho Roh
- Department of Laboratory Medicine, National Health Insurance Service, Ilsan Hospital, Goyang, Korea
| | - Ki Ho Hong
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Namhee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Jaehyeon Lee
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, Korea
| | - Sook Won Ryu
- Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Myung Guk Han
- Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Sang Won Lee
- Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Cheon Kwon Yoo
- Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
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Garcia M, Chessa C, Bourgoin A, Giraudeau G, Plouzeau C, Agius G, Lévêque N, Beby-Defaux A. Comparison of eMAG™ versus NucliSENS ® EasyMAG ® performance on clinical specimens. J Clin Virol 2017; 88:52-57. [PMID: 28160729 PMCID: PMC7185493 DOI: 10.1016/j.jcv.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/27/2016] [Accepted: 01/14/2017] [Indexed: 11/28/2022]
Abstract
eMAG™ is a new nucleic acid extraction platform based on magnetic silica technology. Performance of eMAG™ and easyMAG® were compared on various clinical specimens. Agreement for virus detection ranged from 84.6% to 95.9%. Correlation for virus quantitation displayed R2 from 0.802 to 0.995. The two platforms showed comparable performance on the clinical specimens tested.
Background eMAG™ (bioMerieux) is a new nucleic acid extraction platform based on magnetic silica technology, like its predecessor, NucliSENS® easyMAG® (bioMerieux). Using the same reagents and disposables, eMAG™ adds further automation, allowing simultaneous extraction of 48 samples directly from primary tubes, and distribution of nucleic acid extracts on PCR strips or in tubes at the end of the extraction process. Objective To compare the performance of eMAG™ and easyMAG® on various clinical specimens. Study design Respiratory (n = 199), whole blood (n = 50), plasma (n = 25) and urine (n = 25) specimens were extracted in parallel on both platforms. Both qualitative (respiratory virus, cell control, CMV, EBV, HHV6 and BKV detection) and quantitative (respiratory virus and cell control cycle thresolds, and CMV, EBV, HHV6 and BKV viral loads) results were compared. Results Detection of qualitative targets showed good agreement, ranging from 84.6% for whole blood to 95.9% for respiratory specimens. Correlations between quantitative results were good, with R2 ranging from 0.802 to 0.995. Quantitative results showed average overall differences below 0.10 log10 copies/mL between eMAG™ and easyMAG®. Conclusions The two platforms showed comparable performance on the types of clinical specimen tested. With higher automation and throughput than easyMAG®, the eMAG™ platform is likely to be advantageous for laboratories performing a large number of molecular analyses.
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Affiliation(s)
- Magali Garcia
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France; EA4331-LITEC, Université de Poitiers, Poitiers, France
| | - Céline Chessa
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France; EA4331-LITEC, Université de Poitiers, Poitiers, France
| | - Anne Bourgoin
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France
| | - Geneviève Giraudeau
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France
| | - Chloé Plouzeau
- Laboratoire de Bactériologie, CHU de Poitiers, Poitiers, France; Unité de Microbiologie Moléculaire et Séquençage, CHU de Poitiers, Poitiers, France
| | - Gérard Agius
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France
| | - Nicolas Lévêque
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France; EA4331-LITEC, Université de Poitiers, Poitiers, France.
| | - Agnès Beby-Defaux
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France; Unité de Microbiologie Moléculaire et Séquençage, CHU de Poitiers, Poitiers, France
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Cocuzza CE, Piazza F, Musumeci R, Oggioni D, Andreoni S, Gardinetti M, Fusco L, Frigo M, Banfi P, Rottoli MR, Confalonieri P, Rezzonico M, Ferrò MT, Cavaletti G. Quantitative detection of epstein-barr virus DNA in cerebrospinal fluid and blood samples of patients with relapsing-remitting multiple sclerosis. PLoS One 2014; 9:e94497. [PMID: 24722060 PMCID: PMC3983161 DOI: 10.1371/journal.pone.0094497] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/16/2014] [Indexed: 11/19/2022] Open
Abstract
The presence of Epstein-Barr Virus (EBV) DNA in cerebrospinal fluid (CSF) and peripheral blood (PB) samples collected from 55 patients with clinical and radiologically-active relapsing-remitting MS (RRMS) and 51 subjects with other neurological diseases was determined using standardized commercially available kits for viral nucleic acid extraction and quantitative EBV DNA detection. Both cell-free and cell-associated CSF and PB fractions were analyzed, to distinguish latent from lytic EBV infection. EBV DNA was detected in 5.5% and 18.2% of cell-free and cell-associated CSF fractions of patients with RRMS as compared to 7.8% and 7.8% of controls; plasma and peripheral blood mononuclear cells (PBMC) positivity rates were 7.3% and 47.3% versus 5.8% and 31.4%, respectively. No significant difference in median EBV viral loads of positive samples was found between RRMS and control patients in all tested samples. Absence of statistically significant differences in EBV positivity rates between RRMS and control patients, despite the use of highly sensitive standardized methods, points to the lack of association between EBV and MS disease activity.
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Affiliation(s)
- Clementina E Cocuzza
- Dipartimento di Chirurgia e Medicina Traslazionale, Università di Milano-Bicocca, Monza, Italy
| | - Fabrizio Piazza
- Dipartimento di Chirurgia e Medicina Traslazionale, Università di Milano-Bicocca, Monza, Italy
| | - Rosario Musumeci
- Dipartimento di Chirurgia e Medicina Traslazionale, Università di Milano-Bicocca, Monza, Italy
| | - Davide Oggioni
- Dipartimento di Chirurgia e Medicina Traslazionale, Università di Milano-Bicocca, Monza, Italy
| | - Simona Andreoni
- Dipartimento di Chirurgia e Medicina Traslazionale, Università di Milano-Bicocca, Monza, Italy
| | - Margherita Gardinetti
- Dipartimento di Chirurgia e Medicina Traslazionale, Università di Milano-Bicocca, Monza, Italy
| | - Letizia Fusco
- Dipartimento di Chirurgia e Medicina Traslazionale, Università di Milano-Bicocca, Monza, Italy
| | - Maura Frigo
- Clinica Neurologica, A.O. S. Gerardo, Monza, Italy
| | - Paola Banfi
- Dipartimento di Neurologia, Ospedale di Circolo e Fondazione Macchi, Varese, Italy
| | - Maria R Rottoli
- Centro Sclerosi Multipla, A.O. Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Paolo Confalonieri
- U.O. Neurologia IV, Centro Sclerosi Multipla, Fondazione Istituto Neurologico "Carlo Besta", Milano, Italy
| | | | - Maria T Ferrò
- Centro Sclerosi Multipla, Dipartimento di Neurologia, A.O. Ospedale Maggiore, Crema, Italy
| | - Guido Cavaletti
- Dipartimento di Chirurgia e Medicina Traslazionale, Università di Milano-Bicocca, Monza, Italy
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Sun N, Deng C, Zhao X, Zhou Q, Ge G, Liu Y, Yan W, Xia Q. Extraction of total nucleic acid based on silica-coated magnetic particles for RT-qPCR detection of plant RNA virus/viroid. J Virol Methods 2014; 196:204-11. [DOI: 10.1016/j.jviromet.2013.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/16/2013] [Accepted: 11/20/2013] [Indexed: 10/26/2022]
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High-throughput direct fecal PCR assay for detection of Mycobacterium avium subsp. paratuberculosis in sheep and cattle. J Clin Microbiol 2013; 52:745-57. [PMID: 24352996 DOI: 10.1128/jcm.03233-13] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Johne's disease (JD) is a chronic enteric disease caused by Mycobacterium avium subsp. paratuberculosis that affects ruminants. Transmission occurs by the fecal-oral route. A commonly used antemortem diagnostic test for the detection of M. avium subsp. paratuberculosis in feces is liquid culture; however, a major constraint is the 2- to 3-month incubation period needed for this method. Rapid methods for the detection of M. avium subsp. paratuberculosis based on PCR have been reported, but comprehensive validation data are lacking. We describe here a new test, the high-throughput-Johnes (HT-J), to detect M. avium subsp. paratuberculosis in feces. Its diagnostic accuracy was compared with that of liquid radiometric (Bactec) fecal culture using samples from cattle (1,330 samples from 23 herds) and sheep (596 samples from 16 flocks). The multistage protocol involves the recovery of M. avium subsp. paratuberculosis cells from a fecal suspension, cell rupture by bead beating, extraction of DNA using magnetic beads, and IS900 quantitative PCR. The limit of detection of the assay was 0.0005 pg, and the limit of quantification was 0.005 pg M. avium subsp. paratuberculosis genomic DNA. Only M. avium subsp. paratuberculosis was detected from a panel of 51 mycobacterial isolates, including 10 with IS900-like sequences. Of the 549 culture-negative fecal samples from unexposed herds and flocks, 99% were negative in the HT-J test, while 60% of the bovine- and 84% of the ovine-culture-positive samples were positive in the HT-J test. As similar total numbers of samples from M. avium subsp. paratuberculosis-exposed animals were positive in culture and HT-J tests in both species, and as the results of a McNemar's test were not significant, these methods probably have similar sensitivities, but the true diagnostic sensitivities of these tests are unknown. These validation data meet the consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis and the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines (S. A. Bustin et al., Clin. Chem. 55:611-622, 2009, doi:10.1373/clinchem.2008.112797). The HT-J assay has been approved for use in JD control programs in Australia and New Zealand.
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Verheyen J, Kaiser R, Bozic M, Timmen-Wego M, Maier BK, Kessler HH. Extraction of viral nucleic acids: Comparison of five automated nucleic acid extraction platforms. J Clin Virol 2012; 54:255-9. [DOI: 10.1016/j.jcv.2012.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 02/02/2023]
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Jarvis LM, Mulligan K, Dunsford TH, McGowan K, Petrik J. Suitability of an automated nucleic acid extractor (easyMAG) for use with hepatitis C virus and human immunodeficiency virus type 1 nucleic acid amplification testing. J Virol Methods 2010; 171:364-8. [PMID: 21126541 DOI: 10.1016/j.jviromet.2010.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/16/2010] [Accepted: 11/22/2010] [Indexed: 10/18/2022]
Abstract
Serological screening assays have greatly reduced, but not eliminated, the risk of transmission of viral infections by transfusion of blood and blood products. In addition, the 1999 regulation of the European Agency for the Evaluation of Medicinal Products requiring all plasma for fractionation to have tested negative for hepatitis C virus (HCV) RNA (CPMP/BWP/390/97, 1998) led many blood transfusion services to introduce nucleic acid amplification technology (NAT) to screen blood donations for HCV, and in some services for human immunodeficiency virus (HIV) and hepatitis B virus (HBV). BioMérieux's second-generation system, the NucliSENS easyMAG, was evaluated as a suitable platform for the automated extraction of nucleic acids for use with the existing SNBTS NAT assays. Two nucleic acid extraction protocols were examined, either lysis on the easyMAG (on board) or a 30-min pre-incubation of the sample with lysis buffer at 37 °C (off board). Off board lysis was found to extract nucleic acid more efficiently for both HCV and HIV NAT assays although the improvement was more marked with HIV. The 95% limit of detections (LODs) were 10.11 IU/ml (on board) and 7.21 IU/ml (off board) for HCV and 55.11 IU/ml (on board) and 34.13 (off board) for HIV. Using the more sensitive off board lysis, nucleic acid extraction specificity, robustness and reliability of the easyMAG were examined and over 10,000 Scottish blood donations (in 107 pools of 95 donations) were tested for HCV and HIV in parallel with the existing assay. The results indicate that the easyMAG is a suitable and flexible nucleic acid extraction system, providing high quality nucleic acids and a rapid response alternative to commercial, fully automated, approved blood screening platforms.
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Affiliation(s)
- L M Jarvis
- Scottish National Blood Transfusion Service Transfusion Transmissible Infections Group, Scottish National Blood Transfusion Service, 21 Ellen's Glen Road, Edinburgh EH177QT, United Kingdom.
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