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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
 oraz 
Jinxin Zheng
Jinxin Zheng
   | 12 lis 2022
Polish Journal of Microbiology's Cover Image
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Article Category: Original Paper
Data publikacji: 12 lis 2022
Zakres stron: 499 - 507
Otrzymano: 14 maj 2022
Przyjęty: 30 sie 2022
DOI: https://doi.org/10.33073/pjm-2022-043
Słowa kluczowe
© 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
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+ 38 12 36a
BC– 26 38 21b
Total 64 50
eISSN:
2544-4646
Język:
Angielski
Częstotliwość wydawania:
4 razy w roku
Dziedziny czasopisma:
Life Sciences, Microbiology and Virology
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