Population-based paediatric respiratory infection surveillance: a prospective inception feasibility cohort study

The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity

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.

Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study

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.

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

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.

Guidelines for reporting non-randomised pilot and feasibility studies

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.

Primary care clinicians' views of paediatric respiratory infection surveillance information to inform clinical decision-making: a qualitative study

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.

Respiratory Tract Infections in Children in the Community: Prospective Online Inception Cohort Study

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.