Plasma metagenomic next-generation sequencing of microbial cell-free DNA detects pathogens in patients with suspected infected pancreatic necrosis

Hong, Duck Jin; Wang, Peng; Zhang, Jingzhu; Li, Kaiwei; Ye, Bo; Li, Gang; Zhou, Jing; Tong, Zhihui; Ke, Lu; Shi, Songjing; Li, Weiqin

doi:10.1186/s12879-022-07662-2

Cited by 5 publications

(7 citation statements)

References 36 publications

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“…Numerous reports have demonstrated the presence of circulating cfmDNA in patients with various communicable and non-communicable diseases [7,9,12,14,15,18,19,[21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37]. Moreover, those studies provided information about circulating cfmDNA in healthy humans, as they mostly included healthy control groups.…”

Section: The Presence Of Circulating Cfmdna In Patients and Healthy I...mentioning

confidence: 99%

“…Although circulating cfmDNA was detected in various cohorts of patients with communicable and non-communicable diseases, and in healthy individuals (including studies with stringent negative experimental control reactions and decontamination frameworks) [7,11,12,14,16,17,20,[23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38], the presence of core circulating cell-free microbiome in humans is still the subject of much deliberation. The potential origin of circulating cfmDNA is shown in Figure 1.…”

Section: The Potential Origin Of Circulating Cfmdnamentioning

confidence: 99%

“…It is known that pathogens can directly invade the bloodstream or disseminate through the disruption of endothelial and epithelial barriers [27]. The circulating cfmDNA of clinically relevant pathogens was found in patients with BSIs and deep-seated infections, and its load was reduced during antimicrobial treatment, suggesting that microbial translocation may occur periodically during infections [30][31][32]34,35]. The circulating cell-free microbiome could originate from various body localizations, as infections of the abdomen, lung, genitourinary tract, peripancreatic lymph node, heart, brain, sternum, joint, pancreas, chorion, and amnion were identified in those patients [23,[30][31][32][33][34]37,38].…”

Section: The Potential Origin Of Circulating Cfmdnamentioning

confidence: 99%

“…It is worth noting that circulating cfmDNA may originate simultaneously from various body sites. In a study conducted on patients with suspected infected pancreatic necrosis (IPN), four cases were found of false-positive results of circulating cfmDNA sequencing as compared to the results of peripancreatic drains culture, and the identified pathogens were associated with cholecystitis or ventilator-associated pneumonia [32]. However, active infections may not be the only source of microorganisms.…”

Section: The Potential Origin Of Circulating Cfmdnamentioning

confidence: 99%

“…The sequencing of circulating cfmDNA could also be used for the accurate detection of causative pathogens in other infections [31][32][33][34]36,37]. A recent study showed that the sequencing assay may provide an alternative to conventional cultures and bronchoscopy for the comprehensive identification of secondary pneumonia in COVID-19 patients, and may enable better antibiotic stewardship in those patients [33].…”

Section: Febrile Neutropeniamentioning

confidence: 99%

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Circulating Microbial Cell-Free DNA in Health and Disease

Pietrzak

Kawacka

Olejnik-Schmidt

et al. 2023

IJMS

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Human blood contains low biomass of circulating microbial cell-free DNA (cfmDNA) that predominantly originates from bacteria. Numerous studies have detected circulating cfmDNA in patients with infectious and non-infectious diseases, and in healthy individuals. Remarkable differences were found in the microbial composition of healthy subjects and patients compared to cohorts with various diseases or even patients with diversified prognoses, implying that these alterations may be associated with disease development. Although the function of circulating cfmDNA needs to be elucidated (whether it acts as a bystander of dysbiosis or a key player in disease development), several studies have demonstrated its potential as a non-invasive biomarker that may improve diagnosis and treatment efficacy. The origin of circulating cfmDNA is still the subject of much deliberation, but studies have identified members of various microbiome niches, including the gut, oral cavity, airways, and skin. Further studies investigating the origin and function of circulating cfmDNA are needed. Moreover, low-biomass microbiome studies are prone to contamination, therefore stringent negative experimental control reactions and decontamination frameworks are advised in order to detect genuine circulating cfmDNA.

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Section: The Presence Of Circulating Cfmdna In Patients and Healthy I...mentioning

confidence: 99%

Section: The Potential Origin Of Circulating Cfmdnamentioning

confidence: 99%

Section: The Potential Origin Of Circulating Cfmdnamentioning

confidence: 99%

Section: The Potential Origin Of Circulating Cfmdnamentioning

confidence: 99%

Section: Febrile Neutropeniamentioning

confidence: 99%

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Circulating Microbial Cell-Free DNA in Health and Disease

Pietrzak

Kawacka

Olejnik-Schmidt

et al. 2023

IJMS

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Fragment Ends of Circulating Microbial DNA as Signatures for Pathogen Detection in Sepsis

et al. 2022

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Background Nuclear-derived cell-free DNA (cfDNA) molecules in blood plasma are nonrandomly fragmented, bearing a wealth of information related to tissues of origin. DNASE1L3 (deoxyribonuclease 1 like 3) is an important player in shaping the fragmentation of nuclear-derived cfDNA molecules, preferentially generating molecules with 5′ “CC” dinucleotide termini (i.e., 5′ CC-end motif). However, the fragment end properties of microbial cfDNA and its clinical implication remain to be explored. Methods We performed end motif analysis on microbial cfDNA fragments in plasma samples from patients with sepsis. A sequence context-based normalization method was used to minimize the potential biases for end motif analysis. Results The end motif profiles of microbial cfDNA appeared to resemble that of nuclear cfDNA (Spearman correlation coefficient: 0.82, P value <0.001). The CC-end motif was the most preferred end motif in microbial cfDNA, suggesting that DNASE1L3 might also play a role in the fragmentation of microbe-derived cfDNA in plasma. Of note, differential end motifs were present between microbial cfDNA originating from infection-causing pathogens (enriched at the CC-end) and contaminating microbial DNA potentially derived from reagents or the environment (nearly random). The use of fragment end signatures allowed differentiation between confirmed pathogens and contaminating microbes, with an area under the receiver operating characteristic curve of 0.99. The performance appeared to be superior to conventional analysis based on microbial cfDNA abundance alone. Conclusions The use of fragmentomic features could facilitate the differentiation of underlying contaminating microbes from true pathogens in sepsis. This work demonstrates the potential usefulness of microbial cfDNA fragmentomics in metagenomics analysis.

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Evaluation of the diagnostic utility of metagenomic next-generation sequencing testing for pathogen identification in infected hosts: a retrospective cohort study

Williams,

Webster,

Cai

et al. 2024

Therapeutic Advances in Infection

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Background: Metagenomic next-generation sequencing (mNGS) testing identifies thousands of potential pathogens in a single blood test, though data on its real-world diagnostic utility are lacking. Objectives: Determine the diagnostic utility of mNGS testing in practice and factors associated with high clinical utility. Design: Retrospective cohort study of mNGS tests ordered from June 2018 through May 2020 at a community teaching hospital. Methods: Tests were included if ordered for diagnostic purposes in patients with probable or high clinical suspicion of infection. Exclusions included patient expiration, hospice care, or transfer outside of the institution. Utility criteria were established a priori by the research team. Two investigators independently reviewed each test and categorized it to either high or low diagnostic utility. Reviewer discordance was referred to a third investigator. The stepwise multiple regression method was used to identify clinical factors associated with high diagnostic utility. Results: Among 96 individual tests from 82 unique patients, 80 tests met the inclusion criteria for analysis. At least one potential pathogen was identified in 58% of tests. Among 112 pathogens identified, there were 74 bacteria, 25 viruses, 12 fungi, and 1 protozoon. In all, 46 tests (57.5%) were determined to be of high diagnostic utility. Positive mNGS tests were identified in 36 (78.3%) and 11 (32.4%) of high and low diagnostic utility tests, respectively ( p < 0.001). Antimicrobials were changed after receiving test results in 31 (67.4%) of high utility tests and 4 (11.8%) of low utility tests ( p < 0.0001). In the multiple regression model, a positive test [odds ratio (OR) = 10.9; 95% confidence interval (CI), 3.2–44.4] and consultation with the company medical director (OR = 3.6; 95% CI, 1.1–13.7) remained significantly associated with high diagnostic utility. Conclusion: mNGS testing resulted in high clinical utility in most cases. Positive mNGS tests were associated with high diagnostic utility. Consultation with the Karius® medical director is recommended to maximize utility.

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Plasma metagenomic next-generation sequencing of microbial cell-free DNA detects pathogens in patients with suspected infected pancreatic necrosis

Cited by 5 publications

References 36 publications

Circulating Microbial Cell-Free DNA in Health and Disease

Circulating Microbial Cell-Free DNA in Health and Disease

Fragment Ends of Circulating Microbial DNA as Signatures for Pathogen Detection in Sepsis

Evaluation of the diagnostic utility of metagenomic next-generation sequencing testing for pathogen identification in infected hosts: a retrospective cohort study

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