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Diagnostic performance of metagenomic next-generation sequencing and conventional microbial culture for spinal infection: a retrospective comparative study

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Abstract

Purpose

The study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) as a diagnostic test for biopsy samples from patients with suspected spinal infection (SI) and compared the diagnostic performance of mNGS with that of microbial culture.

Methods

All patients diagnosed with clinical suspicion of SI were enrolled, and data were collected through a retrospective chart review of patient records. Biopsy specimens obtained from each patient were tested via mNGS and microbial culture. Samples were enriched for microbial DNA using the universal DNA extraction kit, whole-genome amplified, and sequenced using MGISEQ-200 instrument. After Low-quality reads removed, the remaining sequences for microbial content were analyzed and aligned using SNAP and kraken2 tools.

Results

A total of 39 patients (19 men and 20 women) were deemed suitable for enrollment. The detection rate for pathogens of mNGS was 71.8% (28/39), which was significantly higher than that of microbial culture (23.1%, p = 0.016). Mycobacterium tuberculosis complex was the most frequently isolated. Using pathologic test as the standard reference for SI, thirty-one cases were classified as infected, and eight cases were considered aseptic. The sensitivity and specificity values for detecting pathogens with mNGS were 87.1% and 87.5%, while these rates were 25.8% and 87.5% with conventional culture. mNGS was able to detect 88.9% (8/9) of pathogens identified by conventional culture, with a genus-level sensitivity of 100% (8/8) and a species-level sensitivity of 87.5% (7/8).

Conclusion

The present work suggests that mNGS might be superior to microbial culture for detecting SI pathogens.

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Acknowledgements

We thank the patients and the patients’ guardians and families for their support. Without their participation, this report could not have been possible; we are very thankful. The mNGS assay was performed by a commercial institution (Guangzhou Daan Clinical Laboratory Center, China).

Funding

One author (ZW) has received funding from Guangdong Basic and Applied Basic Research Foundation (2021A1515011508) and the Scientific Research Start Plan of Shunde Hospital, Southern Medical University (CRSP2019010). Another author (WL) has received funding from the Scientific Research Start Plan of Shunde Hospital, Southern Medical University (SRSP2021007).

Author information

Author notes

  1. Wentao Lin, Faqin Xie, and Xinan Li contributed equally to this work.

Authors and Affiliations

  1. Department of Spine Surgery, Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), No. 1 Jiazi Rd, Shunde District, Foshan City, Guangdong Province, China

    Wentao Lin, Faqin Xie, Ruobing Yang, Junan Lu, Zheng Ruan, Dingqiang Ou & Zhiyun Wang

  2. School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China

    Xinan Li

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Contributions

WL: data curation; funding acquisition; investigation; writing—original draft; FX: data curation; supervision; validation; XL: writing—original draft; RY: data curation; investigation; methodology; project administration; JL: supervision; validation; writing—original draft; ZR: investigation; software; supervision; DO: formal analysis; investigation; methodology; software; ZW: conceptualization; funding acquisition; methodology; project administration; writing—review and editing.

Corresponding author

Correspondence to Zhiyun Wang.

Ethics declarations

Ethics approval

This study was performed in line with the principles of the Declaration of Helsinki. Approval was granted by the Ethics Committee of Shunde Hospital, Southern Medical University (LWLS202201014).

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Informed consent was obtained from all individual participants included in the study.

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The authors have no relevant financial or non-financial interests to disclose.

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Lin, W., Xie, F., Li, X. et al. Diagnostic performance of metagenomic next-generation sequencing and conventional microbial culture for spinal infection: a retrospective comparative study. Eur Spine J 32, 4238–4245 (2023). https://doi.org/10.1007/s00586-023-07928-6

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