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Evaluation of a stepwise approach using microbiota analysis, species-specific qPCRs and culture for the diagnosis of lower respiratory tract infections

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Abstract

In clinical practice, the diagnosis of lower respiratory tract infections (LRTIs) is based on culture. The aim of this study was to evaluate whether a stepwise approach using microbiota analysis, species-specific quantitative real-time (q)PCRs and culture has the potential to be a more accurate and efficient diagnostic approach than culture alone. Sixty-two sputa obtained in a routine clinical setting from patients with a suspected LRTI were included. All sputa were analysed by culture, microbiota analysis based on the 16S ribosomal RNA gene and multiple species-specific qPCRs. Microbiota and culture data were compared to investigate whether cut-off values for microbiota analysis could be determined. For microbiota analysis, a relative abundance of 25% was identified as the cut-off value for the detection of both genera Streptococcus and Haemophilus. Microbiota analysis combined with species-specific qPCRs resulted in a significant increase in the number of positive sputa (73% vs 58%; p = 0.003) as well as in the number of identified pathogens (51 vs 37; p = 0.049) compared to culture. A stepwise approach using microbiota analysis, species-specific qPCRs and culture has the potential to be used in clinical settings for the diagnosis of LRTIs in the near future.

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Acknowledgements

The authors are grateful to Ingrid Poot (DDL Diagnostic Laboratory) for her technical assistance.

Author information

Authors and Affiliations

  1. DDL Diagnostic Laboratory, 2288 ER, Rijswijk, The Netherlands

    Ellen H. A. van den Munckhof, Maurits N. C. de Koning, Wim G. V. Quint & Leen-Jan van Doorn

  2. Department of Medical Microbiology, Haaglanden Medical Centre Bronovo, 2597 AX, The Hague, The Netherlands

    Maurine A. Leverstein-van Hall

  3. Department of Medical Microbiology, Alrijne Hospital, 2334 CK, Leiden, The Netherlands

    Maurine A. Leverstein-van Hall

  4. NMDL-LCPL, 2288 ER, Rijswijk, The Netherlands

    Maurine A. Leverstein-van Hall

Authors
  1. Ellen H. A. van den Munckhof
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  2. Maurits N. C. de Koning
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  3. Wim G. V. Quint
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  4. Leen-Jan van Doorn
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  5. Maurine A. Leverstein-van Hall
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Corresponding author

Correspondence to Ellen H. A. van den Munckhof.

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Conflict of interest

LD and WQ are shareholders of DDL Diagnostic Laboratory. The other authors declare that they have no competing interests.

Ethical approval

For this type of study, formal consent is not required.

Informed consent

Patients were notified that remainders of their samples might be used for evaluation of diagnostic methods. If patients objected, samples were discarded.

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Electronic supplementary material

Supplementary Table S1

Population characteristics (DOCX 23 kb)

Supplementary Table S2

Microbiota analysis data per sample (XLSX 126 kb)

Supplementary Figure S3

Comparison of Culture with Microbiota Analysis combined with Normalised Species-Specific qPCR for Identification of Pathogens in 62 Sputa. For microbiota analysis, a relative abundance of 25% for the genera Streptococcus and Haemophilus was used as cut-off value. (XLSX 68 kb)

Supplementary Table S4

Discrepancy Analysis for 10 Pathogens identified by Culture but not by Microbiota Analysis combined with qPCR. (DOCX 19 kb)

Supplementary Table S5

Discrepancy Analysis for 24 Pathogens detected by Microbiota Analysis combined with qPCR but not by Culture. (DOCX 19 kb)

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van den Munckhof, E.H.A., de Koning, M.N.C., Quint, W.G.V. et al. Evaluation of a stepwise approach using microbiota analysis, species-specific qPCRs and culture for the diagnosis of lower respiratory tract infections. Eur J Clin Microbiol Infect Dis 38, 747–754 (2019). https://doi.org/10.1007/s10096-019-03511-4

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  • DOI: https://doi.org/10.1007/s10096-019-03511-4

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