Dataset Information

Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort.

ABSTRACT: We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequencing of the 16?S rRNA gene V1-V2 variable regions. All swabbing methods were highly accepted. Microbial community structure analysis revealed 846 phylotypes, 46 of which were unique to oropharynx and 164 unique to nares. The calcium alginate tipped swab was found unsuitable for microbiome determinations. Among the remaining three swab types, there were no differences in oropharyngeal microbiomes detected and only marginal differences in nasal microbiomes. Microbial community structures did not differ between staff-collected and self-collected nasal swabs. These results suggest (1) that nasal and oropharyngeal swabbing are highly feasible methods for human population-based studies that include the characterization of microbial community structures in these important ecological niches, and (2) that self-collection of nasal swabs at home can be used to reduce cost and resources needed, particularly when serial measurements are to be taken.

SUBMITTER: Akmatov MK

PROVIDER: S-EPMC5431815 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort.

Akmatov Manas K MK Koch Nadine N Vital Marius M Ahrens Wolfgang W Flesch-Janys Dieter D Fricke Julia J Gatzemeier Anja A Greiser Halina H Günther Kathrin K Illig Thomas T Kaaks Rudolf R Krone Bastian B Kühn Andrea A Linseisen Jakob J Meisinger Christine C Michels Karin K Moebus Susanne S Nieters Alexandra A Obi Nadia N Schultze Anja A Six-Merker Julia J Pieper Dietmar H DH Pessler Frank F

Scientific reports 20170512 1

We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequenci ...[more]

PMID: 28500287

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Project description:Introduction/objectivesLarge scale population-based studies focusing on infectious diseases are scarce. This may be explained by methodological obstacles concerning ascertainment of data on infectious diseases requiring, e.g. collection of data on relatively short-termed symptoms and/or collection of biosamples for pathogen identification during a narrow time window. In the German National Cohort (GNC), a novel self-administered questionnaire will be used in addition to biosampling to collect data on selected infectious diseases and symptoms. The aim of this study was to evaluate in Pretest 2 of the GNC newly added items on self-assessed vulnerability to several infectious diseases and to assess test-retest reliability of the questionnaire.MethodsThe study was conducted in two study centres (Hamburg and Hanover) during Pretest 2 of the GNC. A self-administered paper questionnaire was applied. In Hamburg, participants were asked to fill in the questionnaire during their regular visit at the study centre. For test-retest reliability, participants in Hanover filled in the same questionnaire at home twice. To evaluate agreement, item-related percentage agreement and kappa (κ) were calculated. In addition, we computed Bennet's S and Krippendorf's alpha (α). Items on self-assessed vulnerability to infections were evaluated by comparing them with the corresponding self-reported frequency of infections. An explanatory factor analysis was applied to construct the scores of self-reported infection frequency and self-assessed vulnerability to infections.ResultsThe evaluation of the internal consistency of the five-item instrument of self-assessed vulnerability to infections resulted in a Cronbach's α of 0.78. The factor analysis yielded evidence of one factor. The factor was divided into three groups (lowest quintile classified as "less prone to infections" compared to peers; second, middle and fourth quintiles classified as "similarly prone to infections" and highest quintile classified as "more prone to infections"). Participants classified as "less prone to infections" reported fewer infections than participants classified as "more prone to infections". Spearman's correlation of the two scores (self-reported infection frequency and self-assessed vulnerability to infection) was 0.50 (p < 0.0001). For quantifying reliability, 88 participants with a median time of 8 days between filling in both questionnaires could be included in the analysis; for items sensitive to disease occurrence between both questionnaires only participants with no relevant disease in this time interval were included (n = 75). The weighted κ ranged between 0.65 and 0.87 for the items on infectious disease frequency in the last 12 months, for items on symptom frequency in the past 12 months between 0.77 and 0.90, and for items on vulnerability compared to peers between 0.68 and 0.76.ConclusionA five-item instrument on self-assessed vulnerability to infections seems to be promising, but requires further evaluation. Overall, the questionnaire on self-reported infectious diseases used in Pretest 2 of the GNC is a moderately reliable instrument and, thus, can be applied in future studies on infectious diseases.

Project description:BackgroundData about the vaccination status of participants are required in epidemiological cohort studies whenever infection or immunity is considered as potential exposure or outcome. Within Pretest 2 of the German National Cohort (GNC) we therefore investigated the acceptance and feasibility of extracting vaccination status from vaccination certificates provided by the participants of the study.MethodsThis study was conducted in three study centers (Bremen, n = 73; Hamburg, n = 200; Hannover, n = 193). In order to test if an additional reminder would prevent participants from forgetting their vaccination certificates at home persons willing to participate in Pretest 2 were randomly assigned to one of three invitation groups (IG). About one third of the participants received either no further reminder (IG1), a reminder card together with the appointment letter (IG2) or a separate reminder card 4 days before the appointment (IG3). At the study center, vaccination data were scanned or copied and entered into a database using a unique identification number. Participants were also asked to fill in a short questionnaire to assess the completeness of the provided vaccination data. Additionally, in one of the three participating study centers, general practitioners (GP) were asked to provide vaccination data from their records following respective participants' consent. Finally, we compared the influenza data from the vaccination certificates with the influenza data obtained from participants in Pretest 2 by use of a self-administered questionnaire (ID-Screen).ResultsDue to different starting dates of the study the intended reminder procedure was implemented only in Hamburg and Hannover. In Hamburg, significantly more vaccination certificates were submitted by the group which received the reminder card separately 4 days before the examination (IG3) compared to IG1 and IG2 (p = 0.04). In Hannover, in contrast, most vaccination certificates were brought by those who received the reminder card together with the appointment letter. Overall, the use of a reminder card had a positive but not significant effect as 89 % (185/209) of participants who received the reminder card submitted vaccination data versus 81 % (84/104) of participants who did not receive any reminder card (p = 0.06). Of all Pretest 2 participants in Hannover, 62 % (120/193) gave written consent for data collection by the GPs. In total, 114 practices were contacted of which 49 (43 %) sent vaccination data. All in all, 360 vaccination certificates with 5065 documented vaccinations were entered into a database, of which 4830 (95 %) were valid for analysis covering a period from 1946 to 2012. The comparison of influenza vaccination data from vaccination certificates to the remembered data from a self-completed questionnaire showed an agreement of data in 46 % (84/184) of cases (Kappa = 0.48). Influenza vaccinations were underreported in 4 % (7/170) of self-completed questionnaires.ConclusionThe reliable documentation of vaccinations within the context of the GNC proved to be feasible and thus recommendable at a large scale within the GNC as participants showed high willingness and compliance in providing available vaccination documents. An additional validation by means of documents provided by physicians seems to be possible for more than a quarter of participants. In order to maximize the likelyhood of participants' of bringing their vaccination certificates it would be sufficient to send a reminder card together with the appointment letter.

Dataset Information

Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort.

Publications

Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort.

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