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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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Woodall CA, Hammond A, Cleary D, Preston A, Muir P, Pascoe B, Sheppard SK, Hay AD. Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study. Heliyon 2023; 9:e18610. [PMID: 37593638 PMCID: PMC10432180 DOI: 10.1016/j.heliyon.2023.e18610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
We conducted a feasibility cohort study which aimed to recruit and retain adults from the community to collect saliva (oral) and stool (gut) samples at three time points, at the start of the study (baseline), during a respiratory tract infection (RTI) and post-RTI. Community RTIs place a huge burden on health care services, and a non-invasive microbial diagnostic tool to predict the most vulnerable to respiratory infection would be ideal. To this aim, we analysed oral-gut baseline samples comparing those who reported RTI symptoms to those who remained healthy throughout the study for microbial biomarkers of respiratory susceptibility. Amplicon sequence variants (ASV) were identified by 16S sequence profiling to reveal oral-gut microbes. Reverse transcriptase-polymerase chain reaction (RT-PCR) was applied to target common respiratory microbes. Two general practices were recruited, and the participant recruitment rate was 1.3%. A total of 40 adult participants were retained, of which 19 acquired an RTI whereas 21 remained healthy. In healthy baseline oral and gut samples, ASVs from participants with RTI symptoms compared to those who remained healthy were similar with a high relative abundance of Streptococcus sp., and Blautia sp., respectively. Linear discriminant analysis effect size (LEfSe) revealed baseline oral microbes differed, indicating participants who suffered RTI symptoms had enhanced Streptococcus sobrinus and Megamonas sp., and depletion of Lactobacillus salivarius, Synergistetes, Verrucomicrobia and Dethiosulfovibrio. Furthermore, a random forest model ranked Streptococcus (4.13) as the highest mean decrease in accuracy (MDA) and RT-PCR showed a higher level of carriage of coagulase-negative Staphylococcus. Baseline core gut microbes were similar in both participant groups whereas LEfSe analysis revealed enhanced Veillonella, Rikenellaceae, Enhydobacteria, Eggerthella and Xanthomonsdales and depleted Desulfobulbus and Coprobacillus. Sutterella (4.73) had a high MDA value. Overall, we demonstrated the feasibility of recruiting and retaining adult participants from the community to provide multiple biological samples for microbial profiling. Our analyses identified potential oral-gut microbial biomarkers of respiratory infection susceptibility in otherwise healthy participants.
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Affiliation(s)
- Claire A. Woodall
- School of Cellular and Molecular Medicine, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashley Hammond
- Centre for Academic Primary Care, Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - David Cleary
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Andrew Preston
- The Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Peter Muir
- Public Health England, Southwest Regional Laboratory, National Infection Service, Southmead Hospital, Bristol, UK
| | - Ben Pascoe
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Alastair D. Hay
- Centre for Academic Primary Care, Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
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Prospective Study of the Performance of Parent-Collected Nasal and Saliva Swab Samples, Compared with Nurse-Collected Swab Samples, for the Molecular Detection of Respiratory Microorganisms. Microbiol Spectr 2021; 9:e0016421. [PMID: 34756077 PMCID: PMC8579848 DOI: 10.1128/spectrum.00164-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Respiratory tract infections (RTIs) are ubiquitous among children in the community. A prospective observational study was performed to evaluate the diagnostic performance and quality of at-home parent-collected (PC) nasal and saliva swab samples, compared to nurse-collected (NC) swab samples, from children with RTI symptoms. Children with RTI symptoms were swabbed at home on the same day by a parent and a nurse. We compared the performance of PC swab samples as the test with NC swab samples as the reference for the detection of respiratory pathogen gene targets by reverse transcriptase PCR, with quality assessment using a human gene. PC and NC paired nasal and saliva swab samples were collected from 91 and 92 children, respectively. Performance and interrater agreement (Cohen's κ) of PC versus NC nasal swab samples for viruses combined showed sensitivity of 91.6% (95% confidence interval [CI], 85.47 to 95.73%) and κ of 0.84 (95% CI, 0.79 to 0.88), respectively; the respective values for bacteria combined were 91.4% (95% CI, 86.85 to 94.87%) and κ of 0.85 (95% CI, 0.80 to 0.89). In saliva samples, viral and bacterial sensitivities were lower at 69.0% (95% CI, 57.47 to 79.76%) and 78.1% (95% CI, 71.60 to 83.76%), as were κ values at 0.64 (95% CI, 0.53 to 0.72) and 0.70 (95% CI, 0.65 to 0.76), respectively. Quality assessment for human biological material (18S rRNA) indicated perfect interrater agreement. At-home PC nasal swab samples performed comparably to NC swab samples, whereas PC saliva swab samples lacked sensitivity for the detection of respiratory microbes. IMPORTANCE RTIs are ubiquitous among children. Diagnosis involves a swab sample being taken by a health professional, which places a considerable burden on community health care systems, given the number of cases involved. The coronavirus disease 2019 (COVID-19) pandemic has seen an increase in the at-home self-collection of upper respiratory tract swab samples without the involvement of health professionals. It is advised that parents conduct or supervise swabbing of children. Surprisingly, few studies have addressed the quality of PC swab samples for subsequent identification of respiratory pathogens. We compared NC and PC nasal and saliva swab samples taken from the same child with RTI symptoms, for detection of respiratory pathogens. The PC nasal swab samples performed comparably to NC samples, whereas saliva swab samples lacked sensitivity for the detection of respiratory microbes. Collection of swab samples by parents would greatly reduce the burden on community nurses without reducing the effectiveness of diagnoses.
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Lancaster GA, Thabane L. Guidelines for reporting non-randomised pilot and feasibility studies. Pilot Feasibility Stud 2019; 5:114. [PMID: 31608150 PMCID: PMC6778655 DOI: 10.1186/s40814-019-0499-1] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/10/2019] [Indexed: 01/08/2023] Open
Abstract
As the number of submissions to Pilot and Feasibility Studies increases, there is a need for good quality reporting guidelines to help researchers tailor their reports in a way that is consistent and helpful to other readers. The publication in 2016 of the CONSORT extension to pilot and feasibility trials filled a much-needed gap, but there still remains some uncertainty as to how to report pilot and feasibility studies that are not randomised. This editorial aims to provide some general guidance on how to report the most common types of non-randomised pilot and feasibility studies that are submitted to the journal. We recommend using the CONSORT extension to pilot and feasibility trials as the main reference document—it includes detailed elaboration and explanation of each item, and in most cases, simple adaptation, or non-use of items that are not applicable, will suffice. Several checklists found on the Equator website may provide helpful supplementary guidance, when used alongside the CONSORT extension, and we give some examples.
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Affiliation(s)
- Gillian A Lancaster
- School of Primary, Social and Community Care, Keele University, Newcastle-under-Lyme, UK
| | - Lehana Thabane
- School of Primary, Social and Community Care, Keele University, Newcastle-under-Lyme, UK
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Anderson EC, Kesten JM, Lane I, Hay AD, Moss T, Cabral C. Primary care clinicians' views of paediatric respiratory infection surveillance information to inform clinical decision-making: a qualitative study. BMJ Paediatr Open 2019; 3:e000418. [PMID: 31321318 PMCID: PMC6597489 DOI: 10.1136/bmjpo-2018-000418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/15/2019] [Accepted: 03/26/2019] [Indexed: 11/30/2022] Open
Abstract
AIM To investigate primary care clinicians' views of a prototype locally relevant, real-time viral surveillance system to assist diagnostic decision-making and antibiotic prescribing for paediatric respiratory tract infections (RTI). Clinicians' perspectives on the content, anticipated use and impact were explored to inform intervention development. BACKGROUND Children with RTIs are overprescribed antibiotics. Pressures on primary care and diagnostic uncertainty can lead to decisional biases towards prescribing. We hypothesise that real-time paediatric RTI surveillance data could reduce diagnostic uncertainty and help reduce unnecessary antibiotic prescribing. METHODOLOGY Semistructured one-to-one interviews with 21 clinicians from a range of urban general practitioner surgeries explored the clinical context and views of the prototype system. Transcripts were analysed using thematic analysis. RESULTS Though clinicians self-identified as rational (not over)prescribers, cognitive biases influenced antibiotic prescribing decisions. Clinicians sought to avoid 'anticipated regret' around not prescribing for a child who then deteriorated. Clinicians were not aware of formal infection surveillance information sources (tending to assume many viruses are around), perceiving the information as novel and potentially useful. Perceptions of surveillance information as presented included: not relevant to decision-making/management; useful to confirm decisions post hoc; and increasing risks of missing sick children. Clinicians expressed wariness of using population-level data to influence individual patient decision-making and expressed preference for threat (high-risk) information identified by surveillance, rather than reassuring information about viral RTIs. CONCLUSIONS More work is needed to develop a surveillance intervention if it is to beneficially influence decision-making and antibiotic prescribing in primary care. Key challenges for developing interventions are how to address cognitive biases and how to communicate reassuring information to risk-oriented clinicians.
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Affiliation(s)
- Emma C Anderson
- Centre for Academic Child Health, Bristol Medical School: Population Health Sciences, University of Bristol School of Social and Community Medicine, Bristol, UK
| | - Joanna May Kesten
- NIHR Collaboration for Leadership in Applied Health Research and Care West and NIHR Health Protection Research Unit in Evaluation of Interventions, University of Bristol School of Social and Community Medicine, Bristol, UK
| | - Isabel Lane
- Centre for Academic Primary Care, NIHR School for Primary Care Research, University of Bristol School of Social and Community Medicine, Bristol, UK
| | - Alastair D Hay
- NIHR Health Protection Research Unit in Evaluation of Interventions, Centre for Academic Primary Care, University of Bristol School of Social and Community Medicine, Bristol, UK
| | - Timothy Moss
- Department of Health and Social Sciences, University of the West of England, Bristol, UK
| | - Christie Cabral
- Centre for Academic Primary Care, University of Bristol School of Social and Community Medicine, Bristol, UK
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Hay AD, Anderson E, Ingle S, Beck C, Hollingworth W. Respiratory Tract Infections in Children in the Community: Prospective Online Inception Cohort Study. Ann Fam Med 2019; 17:14-22. [PMID: 30670390 PMCID: PMC6342588 DOI: 10.1370/afm.2327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/09/2018] [Accepted: 09/27/2018] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Describe the duration of symptoms, proportion of parents seeking primary care consultations, and costs for respiratory tract infections (RTIs) of children in the community. METHODS Community-based, online, prospective inception cohort study. General practitioners from socioeconomically diverse practices posted study invitations to parents of 10,310 children aged ≥3 months and <15 years. RESULTS One parent of 485 (4.7%) children in 331 families consented, completed baseline data and symptom diaries, and agreed to medical record review. Compared with nonresponders, responding parent's children were younger (aged 4 vs 6 years) and less socioeconomically deprived. Between February and July 2016, 206 parents reported 346 new RTIs in 259 children. Among the 197 first RTIs reported per family, it took 23 days for 90% (95% CI, 85%-94%) of children to recover. Median symptom duration was longer: in children with primary care consultations (9 days) vs those without consultations (6 days, P = 0.06); children aged <3 years (11 days) vs >3 years (7 days, P <.01); and among children with reported lower RTI symptoms (12 days) vs those with only upper RTI symptoms (8 days, P <.001). Sixteen (8.1%; 95% CI, 4.7%-12.8%) of 197 children had primary care consultations at least once (total 19 consultations), and a similar proportion had time off school or nursery. Sixty of 188 (32%; 95% CI, 25%-39%) parents reported paying for medications for their child's illness. CONCLUSIONS Parents can be advised that RTI symptoms last up to 3 weeks. Policy makers should be aware that parents may seek primary care support in at least 1 in 12 illnesses.
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Affiliation(s)
- Alastair D Hay
- Centre for Academic Primary Care, Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom .,NIHR Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Bristol, United Kingdom
| | - Emma Anderson
- Centre for Child and Adolescent Health, Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom.,NIHR Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Bristol, United Kingdom
| | - Sue Ingle
- NIHR Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Bristol, United Kingdom.,Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Charles Beck
- NIHR Health Protection Research Unit in Evaluation of Interventions, University of Bristol, Bristol, United Kingdom.,Field Epidemiology Service, Public Health England, Bristol, United Kingdom
| | - William Hollingworth
- Bristol Medical School: Population Health Sciences, University of Bristol, Bristol, United Kingdom
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