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Polish Journal of Microbiology
Édition 71 (2022): Edition 4 (December 2022)
Accès libre
Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients
Chaoqin Zhang
Chaoqin Zhang
,
Hang Cheng
Hang Cheng
,
Yuxi Zhao
Yuxi Zhao
,
Jinlian Chen
Jinlian Chen
,
Meng Li
Meng Li
,
Zhijian Yu
Zhijian Yu
,
Xiang Sun
Xiang Sun
,
Peiyu Li
Peiyu Li
,
Yongpeng Shang
Yongpeng Shang
,
Jinmin Ma
Jinmin Ma
et
Jinxin Zheng
Jinxin Zheng
| 12 nov. 2022
Polish Journal of Microbiology
Édition 71 (2022): Edition 4 (December 2022)
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Article Category:
Original Paper
Publié en ligne:
12 nov. 2022
Pages:
499 - 507
Reçu:
14 mai 2022
Accepté:
30 août 2022
DOI:
https://doi.org/10.33073/pjm-2022-043
Mots clés
cell-free DNA
,
next-generation sequencing
,
bacteremia
,
blood culture
,
pathogens
© 2022 Chaoqin Zhang et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
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
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.
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.
Fig. 4
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
Fig. 6
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
Comparison of the consistency of the pathogen identification between cfDNA mNGS and BC.
cfDNA mNGS
+
cfDNA mNGS
–
Consistency
BC
+
38
12
36
a
BC
–
26
38
21
b
Total
64
50