Pneumologie 2023; 77(S 01): S69
DOI: 10.1055/s-0043-1761028
Abstracts

Sample type comparison and IS-pro method assessment for airway microbiome analysis

A Endres
1   Department of Pneumology and Allergology, Department of Internal Medicine I, University Hospital Frankfurt
,
C Reumkens
2   Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (Nutrim), Maastricht University Medical Center (Mumc+)
,
P Savelkoul
2   Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (Nutrim), Maastricht University Medical Center (Mumc+)
,
F Franssen
3   Department of Respiratory Medicine, School of Nutrition and Translational Research in Metabolism (Nutrim), Maastricht University Medical Centre (Mumc+)
,
M Bos
4   Inbiome B.V.
,
D Budding
4   Inbiome B.V.
,
P Stegmeier
5   Genexplain GmbH
,
G Rohde
1   Department of Pneumology and Allergology, Department of Internal Medicine I, University Hospital Frankfurt
,
C Bellinghausen
1   Department of Pneumology and Allergology, Department of Internal Medicine I, University Hospital Frankfurt
› Author Affiliations
 

To study the airway microbiome in large clinical studies, and potentially transfer findings into routine care, an easy-to-use method with short turnaround times would be desirable.

The IS-pro technology (inBiome, the Netherlands) identifies bacterial species based on different lengths of the 16S-23S interspace rDNA regions in combination with phylum specific sequence polymorphisms of the 16S rDNA.

The aims of this study were to compare the results of IS-Pro technique with culture-based microbiological routine, and to compare non-invasive sampling types with lower airway samples.

Nasal swabs, throat swabs and sputum were obtained from 58 patients. Additionally, broncho-alveolar lavage (BAL) fluid was available from 28 of these patients. In total, 280 samples were obtained. The most common diseases were cystic fibrosis (24%) and COPD (22%). At time of sampling, 44% of patients received antibiotic treatment.

The IS-Pro protocol was straight forward and turnaround time (two days) faster than microbiological culture. The median number of detected OTUs with IS-Pro was 15 per sample. Species and genus level identification were low (37.7% unknowns), but all OTUs were classified into phylum groups. Three out of 16 pathogens detected by routine microbiological culture in BAL were automatically identified by the IS-Pro software. Manual peak assignment additionally allowed identification of P. aeruginosa in six of seven samples that tested positive for this pathogen in culture based methods.

Nasal swab samples showed a significant lower richness and α-diversity compared to sputum and throat swab samples. We found no differences in evenness between sample types. Hierarchical clustering based on Bray-Curtis dissimilarity revealed both clustering by patients and sample type. On a sample type level, microbiota composition in throat swabs and sputum samples each showed more similarity to BAL than nasal swabs.

Sputum and throat swabs are better suited sampling types to assess the lower airway microbiome than nasal swabs. IS-Pro is an easy-to-use and fast microbiome analysis technique, potentially useful for large-scale studies. Species assignment must be improved for automated workflow.



Publication History

Article published online:
09 March 2023

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