Investigations on microbiome of the used clinical device revealed many uncultivable newer bacterial species associated with persistent chronic infections

Ashutosh Kumar Amar; Kalaivani Ramakrishnan; Ajit Ramesh Sawant; Karamveer Karamveer; Jagdish Menon; Basant K. Tiwary; Kenchappa Prashanth

doi:10.54034/mic.e1542

Authors

Ashutosh Kumar Amar Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
Kalaivani Ramakrishnan Department of Microbiology, Mahatma Gandhi Medical College and Research Institute, Sri Balaji Vidyapeeth – Deemed University, Pondicherry, India
Ajit Ramesh Sawant Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
Karamveer Karamveer Centre for Bioinformatics, Pondicherry University Pondicherry, India https://orcid.org/0000-0002-5339-3317
Jagdish Menon Department of Orthopaedics, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
Basant K. Tiwary Centre for Bioinformatics, Pondicherry University Pondicherry, India https://orcid.org/0000-0002-8194-5860
Kenchappa Prashanth Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India https://orcid.org/0000-0002-1952-1848

DOI:

https://doi.org/10.54034/mic.e1542

Keywords:

culture-negative infection, Device microbiome, Persistent infection, 16S rRNA gene sequence analysis, metagenome analysis

Abstract

Introduction. Chronic persistent device-related infections (DRIs) often give culture-negative results in a microbiological investigation. In such cases, investigations on the device metagenome might have a diagnostic value. Materials and Methods. The 16SrRNA gene sequence analysis and next-generation sequencing (NGS) of clinical metagenome were performed to detect bacterial diversity on invasive medical devices possibly involved in culture-negative DRIs. Device samples were first subjected to microbiological investigation followed by metagenome analysis. Environmental DNA (e-DNA) isolated from device samples was subjected to 16SrRNA gene amplification followed by Sanger sequencing (n=14). In addition, NGS of the device metagenome was also performed (n=12). Five samples were only common in both methods. Results. Microbial growth was observed in only nine cases; among these, five cases were considered significant growth, and in the remaining four cases, growth was considered either insignificant or contaminated. Culture and sequencing analysis yielded identical results only in six cases. In culture-negative cases, Sanger sequencing of 16SrRNA gene and NGS of 16SrDNA microbiome was able to identify the presence of rarely described human pathogens, namely Streptococcus infantis, Gemella haemolysans, Meiothermus silvanus, Schlegelella aquatica, Rothia mucilaginosa, Serratia nematodiphila, and Enterobacter asburiae, along with some known common nosocomial pathogens. Bacterial species such as M. silvanus and S. nematodiphila that are never reported in human infection were also identified. Conclusions. Results of a small number of diverse samples of this pilot study might lead to a path to study a large number of device samples that may validate the diversity witnessed. The study shows that a culture free, a holistic metagenomic approach using NGS could help identify the pathogens in culture-negative chronic DRIs.

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