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Indraratna AD, Mytton S, Ricafrente A, Millar D, Gorman J, Azzopardi KI, Frost HR, Osowicki J, Steer AC, Skropeta D, Sanderson-Smith ML. A highly sensitive 3base™ assay for detecting Streptococcus pyogenes in saliva during controlled human pharyngitis. Talanta 2024; 276:126221. [PMID: 38776768 DOI: 10.1016/j.talanta.2024.126221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024]
Abstract
Streptococcus pyogenes (Group A Streptococcus; GAS) is a Gram-positive bacterium responsible for substantial human mortality and morbidity. Conventional diagnosis of GAS pharyngitis relies on throat swab culture, a low-throughput, slow, and relatively invasive 'gold standard'. While molecular approaches are becoming increasingly utilized, the potential of saliva as a diagnostic fluid for GAS infection remains largely unexplored. Here, we present a novel, high-throughput, sensitive, and robust speB qPCR assay that reliably detects GAS in saliva using innovative 3base™ technology (Genetic Signatures Limited, Sydney, Australia). The assay has been validated on baseline, acute, and convalescent saliva samples generated from the Controlled Human Infection for Vaccination Against Streptococcus (CHIVAS-M75) trial, in which healthy adult participants were challenged with emm75 GAS. In these well-defined samples, our high-throughput assay outperforms throat culture and conventional qPCR in saliva respectively, affirming the utility of the 3base™ platform, demonstrating the feasibility of saliva as a diagnostic biofluid, and paving the way for the development of novel non-invasive approaches for the detection of GAS and other oropharyngeal pathogens.
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Affiliation(s)
- Anuk D Indraratna
- Molecular Horizons, School of Chemistry & Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, New South Wales, 2522, Australia
| | - Sacha Mytton
- Genetic Signatures Limited, 7 Eliza Street, Newtown, New South Wales, 2042, Australia
| | - Alison Ricafrente
- Genetic Signatures Limited, 7 Eliza Street, Newtown, New South Wales, 2042, Australia
| | - Doug Millar
- Genetic Signatures Limited, 7 Eliza Street, Newtown, New South Wales, 2042, Australia
| | - Jody Gorman
- Molecular Horizons, School of Chemistry & Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, New South Wales, 2522, Australia
| | - Kristy I Azzopardi
- Tropical Diseases, Murdoch Children's Research Institute, 50 Flemington Road, Melbourne, Victoria, 3052, Australia
| | - Hannah R Frost
- Tropical Diseases, Murdoch Children's Research Institute, 50 Flemington Road, Melbourne, Victoria, 3052, Australia
| | - Joshua Osowicki
- Tropical Diseases, Murdoch Children's Research Institute, 50 Flemington Road, Melbourne, Victoria, 3052, Australia; Department of Paediatrics, University of Melbourne, Grattan Street, Melbourne, Victoria, 3010, Australia; Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital Melbourne, 50 Flemington Road, Melbourne, Victoria, 3052, Australia
| | - Andrew C Steer
- Tropical Diseases, Murdoch Children's Research Institute, 50 Flemington Road, Melbourne, Victoria, 3052, Australia; Department of Paediatrics, University of Melbourne, Grattan Street, Melbourne, Victoria, 3010, Australia; Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital Melbourne, 50 Flemington Road, Melbourne, Victoria, 3052, Australia
| | - Danielle Skropeta
- Molecular Horizons, School of Chemistry & Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, New South Wales, 2522, Australia
| | - Martina L Sanderson-Smith
- Molecular Horizons, School of Chemistry & Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, New South Wales, 2522, Australia.
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Laxton CS, Peno C, Hahn AM, Allicock OM, Perniciaro S, Wyllie AL. The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity. THE LANCET. MICROBE 2023; 4:e837-e850. [PMID: 37516121 DOI: 10.1016/s2666-5247(23)00135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 07/31/2023]
Abstract
Despite its prominence in early scientific records, the usefulness of saliva as a respiratory specimen has been de-emphasised over the past century. However, due to its low cost and reliance on specific supply chains and the non-invasive nature of its collection, its benefits over swab-based specimens are again becoming increasingly recognised. These benefits were highlighted over the course of the COVID-19 pandemic, where saliva emerged as a more practical, clinically non-inferior sample type for the detection of SARS-CoV-2 and saw numerous saliva-based diagnostic tests approved for clinical use. Looking forward, as saliva uniquely contains both respiratory secretions and immunological components, it has potentially wide applications, ranging from clinical diagnostics to post-vaccine disease burden and immunity surveillance. This Personal View seeks to summarise the existing evidence for the use of saliva in detecting respiratory pathogens, beyond SARS-CoV-2, as well as detailing methodological factors that can influence sample quality and thus, clinical utility.
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Affiliation(s)
- Claire S Laxton
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chikondi Peno
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Stephanie Perniciaro
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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Fourie E, Bording ES, Euser SM, Badoux P, Haverkort ME, van Houten MA. Nasal discharge: A unique enhanced alternative for the detection of respiratory pathogens in adults. J Med Virol 2023; 95:e29047. [PMID: 37621163 DOI: 10.1002/jmv.29047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/26/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Upper respiratory tract infections are a significant cause of social- and disease burden worldwide. Currently, invasive and uncomfortable molecular detection methods are used for respiratory pathogen detection. We aimed to assess the ability and bearability of a rhinorrhea swab (RS) to detect respiratory pathogens in comparison to the combined nasopharyngeal and oropharyngeal swab (NP/OP). This study was performed at a Public Health Service severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) testing facility between November and December 2022 in the Netherlands. Adults aged 16 years and older, being subjected to a standard of care NP/OP swab with nasal discharge, were included and received an additional RS. Respiratory pathogen detection was evaluated using SARS-CoV-2 polymerase chain reaction (PCR) and multiplex ligation-dependent probe amplification (MLPA) PCR. Bearability was evaluated using visual analog scale (VAS) scores and a questionnaire. A total of 100 adults with a mean age ± SD of 46 ± 16 years were included. The NP/OP swab detected 104 pathogens, the RS 83 pathogens (p < 0.001), and in total 108 respiratory pathogens were identified in 89 adults (89%). The ability to detect respiratory pathogens compared between the RS and the combined NP/OP swab revealed a sensitivity of 82% (95% CI 73%-89%) and specificity of 100% (95% CI 72%-100%). RS were significantly more bearable than the combined NP/OP swab (p value < 0.001). Therefore, nasal discharge found in adults can be used as an adequate reliable medium for respiratory pathogen detection using SARS-CoV-2 PCR and MLPA PCR.
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Affiliation(s)
- Elandri Fourie
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Eva S Bording
- Public Health Services Kennemerland, Haarlem, The Netherlands
| | - Sjoerd M Euser
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Paul Badoux
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | | | - Marlies A van Houten
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
- Department of Pediatrics, Spaarne Gasthuis, Haarlem and Hoofddorp, The Netherlands
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Lowry SA, Wolfe MK, Boehm AB. Respiratory virus concentrations in human excretions that contribute to wastewater: a systematic review and meta-analysis. JOURNAL OF WATER AND HEALTH 2023; 21:831-848. [PMID: 37387346 PMCID: wh_2023_057 DOI: 10.2166/wh.2023.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Concentrations of nucleic acids from a range of respiratory viruses in wastewater solids collected from wastewater treatment plants correlate to clinical data on disease occurrence in the community contributing to the wastewater. Viral nucleic acids enter wastewater from excretions deposited in toilets or drains. To relate measured concentrations in wastewater at a treatment plant to the number of community infections, viral nucleic-acid concentrations in human excretions are needed as inputs to a mass balance model. Here, we carried out a systematic review and meta-analysis to characterize the concentrations and presence of influenza A and B, respiratory syncytial virus, metapneumovirus, parainfluenza virus, rhinovirus, and seasonal coronaviruses in stool, urine, mucus, sputum, and saliva. We identified 220 data sets from 50 articles and reported viral concentrations and presence in these excretions. Data were unevenly distributed across virus type (with the most available for influenza) and excretion type (with the most available for respiratory excretions). Most articles only reported the presence or absence of the virus in a cross-sectional study design. There is a need for more concentration data, including longitudinal data, across all respiratory virus and excretion types. Such data would allow quantitatively linking virus wastewater concentrations to numbers of infected individuals.
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Affiliation(s)
- Sarah A Lowry
- Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA 94305, USA E-mail:
| | - Marlene K Wolfe
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd., Atlanta, GA 30322, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA 94305, USA
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Fourie E, Sijm YEE, Badoux P, Mérelle ME, Haverkort ME, Euser SM, van Houten MA. High detection rate of viral pathogens in nasal discharge in children aged 0 till 5 years. J Med Virol 2023; 95:e28415. [PMID: 36541735 DOI: 10.1002/jmv.28415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/28/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Respiratory tract infections (RTI) in children remain a cause of disease burden worldwide. Nasopharyngeal (NP) & oropharyngeal (OP) swabs are used for respiratory pathogen detection, but hold disadvantages particularly for children, highlighting the importance and preference for a child friendly detection method. We aimed to evaluate the performance and tolerability of a rhinorrhea swab (RS) in detecting viral pathogens when compared to a combined OP(/NP) or mid-turbinate (MT) nasal swab. This study was conducted between September 2021 and July 2022 in the Netherlands. Children aged 0-5 years, with an upper RTI and nasal discharge, were included and received a combined swab and a RS. Multiplex polymerase chain reaction (PCR) and severe acute respiratory syndrome coronavirus-2 PCR were used for viral pathogen detection. Tolerability was evaluated with a questionnaire and visual analog scale (VAS) scores. During 11 months 88 children were included, with a median age of 1.00 year [interquartile range 0.00-3.00]. In total 122 viral pathogens were detected in 81 children (92%). Sensitivity and specificity of the RS compared to a combined swab were respectively 97% (95% confidence interval [CI] 91%-100%) and 78% (95% CI 45%-94%). Rhinorrhea samples detected more pathogens than the (combined) nasal samples, 112 versus 108 respectively. Median VAS scores were significantly lower for the RS in both children (2 vs. 6) and their parents (0 vs. 5). A RS can therefore just as effectively/reliably detect viral pathogens as the combined swab in young children and is better tolerated by both children and their parents/caregivers.
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Affiliation(s)
- Elandri Fourie
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Yara E E Sijm
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Paul Badoux
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Marieke E Mérelle
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | | | - Sjoerd M Euser
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands.,Department of Pediatrics, Spaarne Gasthuis, Hoofddorp, The Netherlands
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Lown M, Miles EA, Fisk HL, Smith KA, Muller I, Maund E, Rogers K, Becque T, Hayward G, Moore M, Little P, Glogowska M, Hay AD, Stuart B, Mantzourani E, Butler C, Bostock J, Davies F, Dickerson I, Thompson N, Francis N. Self-sampling to identify pathogens and inflammatory markers in patients with acute sore throat: Feasibility study. Front Immunol 2022; 13:1016181. [PMID: 36275691 PMCID: PMC9582425 DOI: 10.3389/fimmu.2022.1016181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction Sore throat is a common reason for overuse of antibiotics. The value of inflammatory or biomarkers in throat swab or saliva samples in predicting benefit from antibiotics is unknown. Methods We used the ‘person-based approach’ to develop an online tool to support self-swabbing and recruited adults and children with sore throats through participating general practices and social media. Participants took bacterial and viral swabs and a saliva sponge swab and passive drool sample. Bacterial swabs were cultured for streptococcus (Group A, B, C, F and G). The viral swab and saliva samples were tested using a routine respiratory panel PCR and Covid-19 PCR testing. We used remaining viral swab and saliva sample volume for biomarker analysis using a panel of 13 biomarkers. Results We recruited 11 asymptomatic participants and 45 symptomatic participants. From 45 symptomatic participants, bacterial throat swab, viral throat swab, saliva sponge and saliva drool samples were returned by 41/45 (91.1%), 43/45 (95.6%), 43/45 (95.6%) and 43/45 (95.6%) participants respectively. Three saliva sponge and 6 saliva drool samples were of insufficient quantity. Two adult participants had positive bacterial swabs. Six participants had a virus detected from at least one sample (swab or saliva). All of the biomarkers assessed were detectable from all samples where there was sufficient volume for testing. For most biomarkers we found higher concentrations in the saliva samples. Due to low numbers, we were not able to compare biomarker concentrations in those who did and did not have a bacterial pathogen detected. We found no evidence of a difference between biomarker concentrations between the symptomatic and asymptomatic participants but the distributions were wide. Conclusions We have demonstrated that it is feasible for patients with sore throat to self-swab and provide saliva samples for pathogen and biomarker analysis. Typical bacterial and viral pathogens were detected but at low prevalence rates. Further work is needed to determine if measuring biomarkers using oropharyngeal samples can help to differentiate between viral and bacterial pathogens in patients classified as medium or high risk using clinical scores, in order to better guide antibiotic prescribing and reduce inappropriate prescriptions.
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Affiliation(s)
- Mark Lown
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
- *Correspondence: Mark Lown,
| | - Elizabeth A. Miles
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Helena L. Fisk
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kirsten A. Smith
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Ingrid Muller
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Emma Maund
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Kirsty Rogers
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Taeko Becque
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Gail Hayward
- Nuffield Department of Primary Care, University of Oxford, Oxford, United Kingdom
| | - Michael Moore
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Paul Little
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Margaret Glogowska
- Nuffield Department of Primary Care, University of Oxford, Oxford, United Kingdom
| | - Alastair D. Hay
- Centre for Academic Primary Care, National Institute for Health Research (NIHR) School for Primary Care Research, Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Beth Stuart
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Efi Mantzourani
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Chris Butler
- Nuffield Department of Primary Care, University of Oxford, Oxford, United Kingdom
| | - Jennifer Bostock
- Southampton Primary Care Research Centre, Patient and Public Involvement Representative, Southampton, United Kingdom
| | - Firoza Davies
- Southampton Primary Care Research Centre, Patient and Public Involvement Representative, Southampton, United Kingdom
| | - Ian Dickerson
- Southampton Primary Care Research Centre, Patient and Public Involvement Representative, Southampton, United Kingdom
| | - Natalie Thompson
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Nick Francis
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
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Salivary Interleukin-6 and C-Reactive Protein/Mean Platelet Volume Ratio in the Diagnosis of Late-Onset Neonatal Pneumonia. J Immunol Res 2021; 2021:8495889. [PMID: 34708133 PMCID: PMC8545599 DOI: 10.1155/2021/8495889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Neonatal pneumonia is a serious respiratory infectious disease with a high rate of case fatality in developing countries. Salivary cytokines could serve as interesting noninvasive markers in the diagnosis of neonatal pneumonia. The aim was to assess the diagnostic role of salivary and serum interleukin-6 (IL-6), C-reactive protein/mean platelet volume (CRP/MPV) ratio, and the combination of these markers in the diagnosis of late-onset neonatal pneumonia in full-term neonates. Seventy full-term neonates, 35 with late-onset neonatal pneumonia and 35 controls, were enrolled in this prospective case-control study. Complete blood count (CBC), salivary and serum IL-6, and CRP concentrations were measured for all the study subjects. The sensitivity, specificity, positive predictive value, and negative predictive value of salivary IL-6, serum IL-6, and CRP/MPV ratio for the diagnosis of late-onset neonatal pneumonia were determined. At the cutoff point of >34 pg/ml, salivary IL-6 showed 82.86% sensitivity and 91.43% specificity. CRP/MPV ratio showed a sensitivity of 97.14% and specificity of 85.71% at a cutoff value > 0.88. The combination of salivary IL-6 and CRP/MPV ratio improved the sensitivity and specificity to 100%. The current study shows for the first time that both salivary IL-6 and CRP/MPV ratio are suitable markers for the diagnosis of late-onset neonatal pneumonia in full-term neonates.
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