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Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients Cover

Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients

Polish Journal of Microbiology
Volume 71 (2022): Issue 4 (December 2022)
By: Chaoqin Zhang,  Hang Cheng,  Yuxi Zhao,  Jinlian Chen,  Meng Li,  Zhijian Yu,  Xiang Sun,  Peiyu Li,  Yongpeng Shang,  Jinmin Ma and  Jinxin Zheng  
Open Access
|Nov 2022

Figures & Tables

Fig. 1

a) Comparison of cfDNA reads number/concentrations (copies/ml) of pathogens by cfDNA mNGS between plasma and serum; b) comparison of cfDNA read numbers/concentrations (copies/ml) between BC+ and BC–; c) comparison of the microbes-derivative cfDNA reads/total cfDNA reads between BC+ and BC– patients. *** – p < 0.001, NS – not significant, BC – blood culture, cfDNA mNGS – cell-free DNA metagenomics next-generation sequencing, + – positive, – – negative
a) Comparison of cfDNA reads number/concentrations (copies/ml) of pathogens by cfDNA mNGS between plasma and serum; b) comparison of cfDNA read numbers/concentrations (copies/ml) between BC+ and BC–; c) comparison of the microbes-derivative cfDNA reads/total cfDNA reads between BC+ and BC– patients. *** – p < 0.001, NS – not significant, BC – blood culture, cfDNA mNGS – cell-free DNA metagenomics next-generation sequencing, + – positive, – – negative

Fig. 2

The relative abundance of cfDNA mNGS-detected bacteria and viruses in the 114 samples were shown by Heatmap. The relative abundance data used in the heatmap were log2‑transformed to compare among species. Staphylococcus epidermidis and Propionibacterium acnes were discarded as contaminants in the downstream analysis.
The relative abundance of cfDNA mNGS-detected bacteria and viruses in the 114 samples were shown by Heatmap. The relative abundance data used in the heatmap were log2‑transformed to compare among species. Staphylococcus epidermidis and Propionibacterium acnes were discarded as contaminants in the downstream analysis.

Fig. 3

Relative abundances of read numbers of microbial species between the BC+ and BC– samples. Confidence intervals and p-values are indicated for each species, and the differences in proportions were calculated as the mean proportion of BC– minus BC+ samples with 95% confidence intervals.
Relative abundances of read numbers of microbial species between the BC+ and BC– samples. Confidence intervals and p-values are indicated for each species, and the differences in proportions were calculated as the mean proportion of BC– minus BC+ samples with 95% confidence intervals.

Fig. 4

Microbial compositions of the BC+ and BC– samples.a) At phylum level; b) at class level.
Microbial compositions of the BC+ and BC– samples.a) At phylum level; b) at class level.

Fig. 5

Comparison of community compositions at the order, family and genus levels. Confidence intervals and p-values are indicated in each case, and the difference in proportions was calculated by the mean proportion of BC– minus BC+ samples with 95% confidence intervals.BC – blood culture, + – positive, – – negative
Comparison of community compositions at the order, family and genus levels. Confidence intervals and p-values are indicated in each case, and the difference in proportions was calculated by the mean proportion of BC– minus BC+ samples with 95% confidence intervals.BC – blood culture, + – positive, – – negative

Fig. 6

Antibiotic treatments and relative pathogen abundances at different times after disease onset.
Antibiotic treatments and relative pathogen abundances at different times after disease onset.

Fig. 7

Patient symptoms with antibiotic treatment.WBC – white blood cells, CRP – C-reactive protein, PCT – procalcitonin, MRSA – methicillin-resistant S. aureus, NGS – cell-free DNA metagenomics next-generation sequencing
Patient symptoms with antibiotic treatment.WBC – white blood cells, CRP – C-reactive protein, PCT – procalcitonin, MRSA – methicillin-resistant S. aureus, NGS – cell-free DNA metagenomics next-generation sequencing

Comparison of the consistency of the pathogen identification between cfDNA mNGS and BC_

cfDNA mNGS+cfDNA mNGS–Consistency
BC+381236a
BC–263821b
Total6450
DOI: https://doi.org/10.33073/pjm-2022-043 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331
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Language: English
Page range: 499 - 507
Submitted on: May 14, 2022
Accepted on: Aug 30, 2022
Published on: Nov 12, 2022
Published by: Polish Society of Microbiologists
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
cell-free DNA,
next-generation sequencing,
bacteremia,
blood culture,
pathogens
Related subjects:
Life sciences,
Microbiology and virology

© 2022 Chaoqin Zhang, Hang Cheng, Yuxi Zhao, Jinlian Chen, Meng Li, Zhijian Yu, Xiang Sun, Peiyu Li, Yongpeng Shang, Jinmin Ma, Jinxin Zheng, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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