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German EL, Nabwera HM, Robinson R, Shiham F, Liatsikos K, Parry CM, McNamara C, Kattera S, Carter K, Howard A, Pojar S, Hamilton J, Matope A, Read JM, Allen SJ, Hill H, Hawcutt DB, Urban BC, Collins AM, Ferreira DM, Nikolaou E. Participant perceptions and experiences of a novel community-based respiratory longitudinal sampling method in Liverpool, UK: A mixed methods feasibility study. PLoS One 2023; 18:e0294133. [PMID: 37943741 PMCID: PMC10635470 DOI: 10.1371/journal.pone.0294133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
Longitudinal, community-based sampling is important for understanding prevalence and transmission of respiratory pathogens. Using a minimally invasive sampling method, the FAMILY Micro study monitored the oral, nasal and hand microbiota of families for 6 months. Here, we explore participant experiences and opinions. A mixed methods approach was utilised. A quantitative questionnaire was completed after every sampling timepoint to report levels of discomfort and pain, as well as time taken to collect samples. Participants were also invited to discuss their experiences in a qualitative structured exit interview. We received questionnaires from 36 families. Most adults and children >5y experienced no pain (94% and 70%) and little discomfort (73% and 47% no discomfort) regardless of sample type, whereas children ≤5y experienced variable levels of pain and discomfort (48% no pain but 14% hurts even more, whole lot or worst; 38% no discomfort but 33% moderate, severe, or extreme discomfort). The time taken for saliva and hand sampling decreased over the study. We conducted interviews with 24 families. Families found the sampling method straightforward, and adults and children >5y preferred nasal sampling using a synthetic absorptive matrix over nasopharyngeal swabs. It remained challenging for families to fit sampling into their busy schedules. Adequate fridge/freezer space and regular sample pick-ups were found to be important factors for feasibility. Messaging apps proved extremely effective for engaging with participants. Our findings provide key information to inform the design of future studies, specifically that self-sampling at home using minimally invasive procedures is feasible in a family context.
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Affiliation(s)
- Esther L. German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Helen M. Nabwera
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - Ryan Robinson
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Farah Shiham
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kostas Liatsikos
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | | | | | | | - Katie Carter
- Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - Ashleigh Howard
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Sherin Pojar
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Joshua Hamilton
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Agnes Matope
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jonathan M. Read
- Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Stephen J. Allen
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Edward Francis Small Teaching Hospital, Banjul, The Gambia
| | - Helen Hill
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Daniel B. Hawcutt
- Alder Hey Children’s Hospital, Liverpool, United Kingdom
- University of Liverpool, Liverpool, United Kingdom
| | - Britta C. Urban
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Andrea M. Collins
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Daniela M. Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Elissavet Nikolaou
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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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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Wyllie AL, Rots NY, Wijmenga-Monsuur AJ, van Houten MA, Sanders EAM, Trzciński K. Saliva as an alternative sample type for detection of pneumococcal carriage in young children. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001394. [PMID: 37819029 PMCID: PMC10634364 DOI: 10.1099/mic.0.001394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
For children, the gold standard for the detection of pneumococcal carriage is conventional culture of a nasopharyngeal swab. Saliva, however, has a history as one of the most sensitive methods for surveillance of pneumococcal colonization and has recently been shown to improve carriage detection in older age groups. Here, we compared the sensitivity of paired nasopharyngeal and saliva samples from PCV7-vaccinated 24-month-old children for pneumococcal carriage detection using conventional and molecular detection methods. Nasopharyngeal and saliva samples were collected from 288 24-month-old children during the autumn/winter, 2012/2013. All samples were first processed by conventional diagnostic culture. Next, DNA extracted from all plate growth was tested by qPCR for the presence of the pneumococcal genes piaB and lytA and a subset of serotypes. By culture, 161/288 (60 %) nasopharyngeal swabs tested positive for pneumococcus, but detection was not possible from saliva due to abundant polymicrobial growth on culture plates. By qPCR, 155/288 (54 %) culture-enriched saliva samples and 187/288 (65 %) nasopharyngeal swabs tested positive. Altogether, 219/288 (76 %) infants tested positive for pneumococcus, with qPCR-based carriage detection of culture-enriched nasopharyngeal swabs detecting significantly more carriers compared to either conventional culture (P<0.001) or qPCR detection of saliva (P=0.002). However, 32/219 (15 %) carriers were only positive in saliva, contributing significantly to the overall number of carriers detected (P=0.002). While testing nasopharyngeal swabs by qPCR proved most sensitive for pneumococcal detection in infants, saliva sampling could be considered as complementary to provide additional information on carriage and serotypes that may not be detected in the nasopharynx and may be particularly useful in longitudinal studies, requiring repeated sampling of study participants.
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Affiliation(s)
- Anne L. Wyllie
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nynke Y. Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Alienke J. Wijmenga-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Elisabeth A. M. Sanders
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Krzysztof Trzciński
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
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Miellet WR, Pluister G, Sikking M, Tappel M, Karczewski J, Visser LJ, Bosch T, Trzciński K, Mariman R. Surveillance of Neisseria meningitidis carriage four years after menACWY vaccine implementation in the Netherlands reveals decline in vaccine-type and rise in genogroup e circulation. Vaccine 2023:S0264-410X(23)00781-8. [PMID: 37423800 DOI: 10.1016/j.vaccine.2023.06.078] [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: 02/21/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
Carriage of Neisseria meningitidisis an accepted endpoint in monitoring meningococcal vaccine effects. We applied molecular methods to assess the impact of menACWY vaccine implementation on meningococcal carriage and genogroup-specific prevalence in young adults in Fall of 2022, four years after the introduction of the tetravalent vaccine in the Netherlands. The overall carriage rate of genogroupable meningococci was not significantly different compared to a pre-menACWY cohort investigated in 2018 (20.8 % or 125 of 601 versus 17.4 % or 52 of 299 individuals, p = 0.25). Of 125 carriers of genogroupable meningococci, 122 (97.6 %) were positive for either vaccine-types menC, menW, menY or genogroups, menB, menE, and menX, which are not targeted by the menACWY vaccine. Compared with a pre-vaccine-implementation cohort, there was 3.8-fold reduction (p < 0.001) in vaccine-type carriage rates and 9.0-fold increase (p < 0.0001) in non-vaccine type menE prevalence. We observe a reduction in menW and menY and an increase in menE, which suggest that implementation of menACWY vaccine affected carriage.
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Affiliation(s)
- Willem R Miellet
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, the Netherlands
| | - Gerlinde Pluister
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Meike Sikking
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marcia Tappel
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Linda J Visser
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Thijs Bosch
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, the Netherlands
| | - Rob Mariman
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
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Miellet WR, van Veldhuizen J, Litt D, Mariman R, Wijmenga-Monsuur AJ, Badoux P, Nieuwenhuijsen T, Thombre R, Mayet S, Eletu S, Sheppard C, van Houten MA, Rots NY, Miller E, Fry NK, Sanders EAM, Trzciński K. It Takes Two to Tango: Combining Conventional Culture With Molecular Diagnostics Enhances Accuracy of Streptococcus pneumoniae Detection and Pneumococcal Serogroup/Serotype Determination in Carriage. Front Microbiol 2022; 13:859736. [PMID: 35509314 PMCID: PMC9060910 DOI: 10.3389/fmicb.2022.859736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background The specificity of molecular methods for the detection of Streptococcus pneumoniae carriage is under debate. We propose a procedure for carriage surveillance and vaccine impact studies that increases the accuracy of molecular detection of live pneumococci in polymicrobial respiratory samples. Methods Culture and qPCR methods were applied to detect pneumococcus and pneumococcal serotypes in 1,549 nasopharyngeal samples collected in the Netherlands (n = 972) and England (n = 577) from 946 toddlers and 603 adults, and in paired oropharyngeal samples collected exclusively from 319 Dutch adults. Samples with no live pneumococci isolated at primary diagnostic culture yet generating signal specific for pneumococcus in qPCRs were re-examined with a second, qPCR-guided culture. Optimal Cq cut-offs for positivity in qPCRs were determined via receiver operating characteristic (ROC) curve analysis using isolation of live pneumococci from the primary and qPCR-guided cultures as reference. Results Detection of pneumococcus and pneumococcal serotypes with qPCRs in cultured (culture-enriched) nasopharyngeal samples exhibited near-perfect agreement with conventional culture (Cohen’s kappa: 0.95). Molecular methods displayed increased sensitivity of detection for multiple serotype carriage, and implementation of qPCR-guided culturing significantly increased the proportion of nasopharyngeal and oropharyngeal samples from which live pneumococcus was recovered (p < 0.0001). For paired nasopharyngeal and oropharyngeal samples from adults none of the methods applied to a single sample type exhibited good agreement with results for primary and qPCR-guided nasopharyngeal and oropharyngeal cultures combined (Cohens kappa; 0.13–0.55). However, molecular detection of pneumococcus displayed increased sensitivity with culture-enriched oropharyngeal samples when compared with either nasopharyngeal or oropharyngeal primary cultures (p < 0.05). Conclusion The accuracy of pneumococcal carriage surveillance can be greatly improved by complementing conventional culture with qPCR and vice versa, by using results of conventional and qPCR-guided cultures to interpret qPCR data. The specificity of molecular methods for the detection of live pneumococci can be enhanced by incorporating statistical procedures based on ROC curve analysis. The procedure we propose for future carriage surveillance and vaccine impact studies improves detection of pneumococcal carriage in adults in particular and enhances the specificity of serotype carriage detection.
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Affiliation(s)
- Willem R Miellet
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Janieke van Veldhuizen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - David Litt
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Rob Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Alienke J Wijmenga-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Paul Badoux
- Regional Laboratory of Public Health (Streeklab) Haarlem, Haarlem, Netherlands
| | - Tessa Nieuwenhuijsen
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
| | - Rebecca Thombre
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Sanaa Mayet
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Seyi Eletu
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Carmen Sheppard
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | | | - Nynke Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Elizabeth Miller
- Immunisation and Countermeasures Division, Public Health England (PHE) - National Infection Service, London, United Kingdom
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom.,Immunisation and Countermeasures Division, Public Health England (PHE) - National Infection Service, London, United Kingdom
| | - Elisabeth A M Sanders
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
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