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Comparative Study
. 2017 Sep 19;17(1):631.
doi: 10.1186/s12879-017-2727-8.

Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study

Lalanika M Abayasekara  1 , Jennifer Perera  2   3 , Vishvanath Chandrasekharan  4   3 , Vaz S Gnanam  3 , Nisala A Udunuwara  3 , Dileepa S Liyanage  3 , Nuwani E Bulathsinhala  3 , Subhashanie Adikary  3 , Janith V S Aluthmuhandiram  3 , Chrishanthi S Thanaseelan  3 , D Portia Tharmakulasingam  3 , Tharaga Karunakaran  3 , Janahan Ilango  3
Affiliations
Comparative Study

Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study

Lalanika M Abayasekara et al. BMC Infect Dis. .

Abstract

Background: Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others. However, to date there has been no commercial application of this technology in infectious disease diagnostic settings.

Methods: Credence Genomics Rapid Infection Detection™ test, is a molecular based diagnostic test that uses next generation sequencing of bacterial 16S rRNA gene and fungal ITS1 gene region to provide accurate identification of species within a clinical sample. Here we present a study comparing 16S and ITS1 metagenomic identification against conventional culture for clinical samples. Using culture results as gold standard, a comparison was conducted using patient specimens from a clinical microbiology lab.

Results: Metagenomics based results show a 91.8% concordance rate for culture positive specimens and 52.8% concordance rate with culture negative samples. 10.3% of specimens were also positive for fungal species which was not investigated by culture. Specificity and sensitivity for metagenomics analysis is 91.8 and 52.7% respectively.

Conclusion: 16S based metagenomic identification of bacterial species within a clinical specimen is on par with conventional culture based techniques and when coupled with clinical information can lead to an accurate diagnostic tool for infectious disease diagnosis.

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Conflict of interest statement

Ethics approval and consent to participate

Though human derived samples will be used, no human DNA from the patients will be used in this study. Specimens will not be expressly collected for this study but rather remnants of commercial culture specimens will be used for validation. Only bacterial or fungal DNA isolated from these specimens will be used in the study.

Application for ethical review was submitted to SICER accredited Ethical Review Committee, Faculty of Medicine, University of Colombo (Reference EC-16-134). Study protocol was approved on 11th August 2016.

Consent for publication

Not Applicable.

Competing interests

Financial: This study was sponsored by Credence Genomics Pvt. Ltd. for validation of commercial NGS-based testing product. Author VSG is the CEO/Managing Director of Credence Genomics Pvt. Ltd.

Authors LMA, NAU, BNE, CST are employees of Credence Genomics Pvt. Ltd. SA, DSL, JVSA, DPT, TK and IJ are past employees of Credence Genomics Pvt. Ltd.

Author VC is affiliated with Credence Genomics Pvt. Ltd. as a consultant in molecular biology.

Author J.P is affiliated with the University of Colombo as the Professor of Microbiology, and specialist Medical Microbiologist at Nawaloka Metropolis laboratory. JP is also affiliated with Credence Genomics Pvt. Ltd. as a specialist in Medical Microbiology.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Phylogenetic tree of urine specimen (a) nasogastric aspiration specimen (b) and pus swab (c). Numbers displayed next to the species in the final branches of the phylogenetic tree indicate the number of reads successfully aligned to the reference 16S rRNA sequence of this species
Fig. 2
Fig. 2
The types and numbers of different clinical specimens used in the analysis (n = 103)
See this image and copyright information in PMC

References

    1. The Human Microbiome. Human Microbiome RSS. Available from: https://www.hmpdacc.org/overview/about/. Accessed on 5 Feb 2017.
    1. World Health Organization. The top 10 causes of death. Available from: http://www.who.int/mediacentre/factsheets/fs310/en/. Accessed on 16 Feb 2017.
    1. Stewart EJ. Growing Unculturable bacteria. J Bacteriol. 2012;194:4151–4160. doi: 10.1128/JB.00345-12. - DOI - PMC - PubMed
    1. Nishie M, Nagao J-I, Sonomoto K. Antibacterial peptides “Bacteriocins”: an overview of their diverse characteristics and applications. Biocont Sci. 2012;17(1):1–16. doi: 10.4265/bio.17.1. - DOI - PubMed
    1. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Nat Acad Sci. 1985;82(20):6955–6959. doi: 10.1073/pnas.82.20.6955. - DOI - PMC - PubMed

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