Dataset Information

Comprehensive characterization of plasma cell-free Echinococcus spp. DNA in echinococcosis patients using ultra-high-throughput sequencing.

ABSTRACT: BACKGROUND:Echinococcosis is a life-threatening parasitic disease caused by Echinococcus spp. tapeworms with over one million people affected globally at any time. The Echinococcus spp. tapeworms in the human body release DNA to the circulatory system, which can be a biomarker for echinococcosis. Cell-free DNA (cfDNA) is widely used in medical research and has been applied in various clinical settings. As for echinococcosis, several PCR-based tests had been trialed to detect cell-free Echinococcus spp. DNA in plasma or serum, but the sensitivity was about 20% to 25%. Low sensitivity of PCR-based methods might be related to our limited understanding of the features of cell-free Echinococcus spp. DNA in plasma, including its concentration, fragment pattern and release source. In this study, we applied ultra-high-throughput sequencing to comprehensively investigate the characteristics of cell-free Echinococcus spp. DNA in plasma of echinococcosis patients. METHODOLOGY/PRINCIPAL FINDINGS:We collected plasma samples from 23 echinococcosis patients. Total plasma cfDNA was extracted and sequenced with a high-throughput sequencing platform. An average of 282 million read pairs were obtained for each plasma sample. Sequencing data were analyzed with bioinformatics workflow combined with Echinococcus spp. sequence database. After identification of cell-free Echinococcus spp. reads, we found that the cell-free Echinococcus spp. reads accounted for 1.8e-5 to 4.0e-9 of the total clean reads. Comparing fragment length distribution of cfDNA between Echinococcus spp. and humans showed that cell-free Echinococcus spp. DNA of cystic echinococcosis (CE) had a broad length range, while that of alveolar echinococcosis (AE) had an obvious peak at about 135 bp. We found that most of the cell-free Echinococcus spp. DNA reads were from the nuclear genome with an even distribution, which might indicate a random release pattern of cell-free Echinococcus spp. DNA. CONCLUSIONS/SIGNIFICANCE:With ultra-high-throughput sequencing technology, we analyzed the concentration, fragment length, release source, and other characteristics of cell-free Echinococcus spp. DNA in the plasma of echinococcosis patients. A better understanding of the characteristics of cell-free Echinococcus spp. DNA in plasma may facilitate their future application as a biomarker for diagnosis.

SUBMITTER: Ji J

PROVIDER: S-EPMC7209354 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Comprehensive characterization of plasma cell-free Echinococcus spp. DNA in echinococcosis patients using ultra-high-throughput sequencing.

Ji Jingkai J Li Bin B Li Jingzhong J Danzeng Wangmu W Li Jiandong J Zhao Yanping Y Qiangba Gezhen G Zhang Qingda Q Renzhen Nibu N Basang Zhuoga Z Jia Changlin C Gongsang Quzhen Q Ma Jinmin J Wang Yicong Y Chen Fang F Zhou Hongcheng H Huasang Yin Jiefang J Xie Jiandan J Pei Na N Cai Huimin H Jiang Huayan H Yang Huanming H Wang Jian J Asan Han Xiumin X Li Junhua J Chen Weijun W Yang Dong D

PLoS neglected tropical diseases 20200413 4

<h4>Background</h4>Echinococcosis is a life-threatening parasitic disease caused by Echinococcus spp. tapeworms with over one million people affected globally at any time. The Echinococcus spp. tapeworms in the human body release DNA to the circulatory system, which can be a biomarker for echinococcosis. Cell-free DNA (cfDNA) is widely used in medical research and has been applied in various clinical settings. As for echinococcosis, several PCR-based tests had been trialed to detect cell-free Ec ...[more]

PMID: 32282820

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Project description:BACKGROUND:Cystic echinococcosis (CE) and alveolar echinococcosis (AE) are highly endemic in Xiji County of Ningxia Hui Autonomous Region (NHAR) in China where the control campaign based on dog de-worming with praziquantel has been undertaken over preceding decades. This study is to determine the current prevalence of Echinococcus granulosus and E. multilocularis in domestic dogs and monitor the echinococcosis transmission dynamics. METHODS:Study villages were selected using landscape patterns (Geographic Information System, GIS) for Echinococcus transmission "hot spots", combined with hospital records identifying risk areas for AE and CE. A survey of 750 domestic dogs, including copro-sampling and owner questionnaires, from 25 selected villages, was undertaken in 2012. A copro-multiplex PCR assay was used for the specific diagnosis of E. granulosus and E. multilocularis in the dogs. Data analysis, using IBM SPSS Statistics, was undertaken, to compare the prevalence of the two Echinococcus spp. in dogs between four geographical areas of Xiji by the ?2 test. Univariate analysis of the combinations of outcomes from the questionnaire and copro-PCR assay data was carried out to determine the significant risk factors for dog infection. RESULTS:The highest de-worming rate of 84.0% was found in the northwest area of Xiji County, and significant differences (P?<? 0.05) in the de-worming rates among dogs from the four geographical areas of Xiji were detected. The highest prevalence (19.7%, 59/300) of E. multilocularis occurred in northwest Xiji, though the highest prevalence (18.1%, 38/210) of E. granulosus occurred in southwest Xiji. There was no significant difference (P?>? 0.05) in the prevalence of E. granulosus in dogs from the northwest, southwest, northeast, and southeast of Xiji, but there were significant differences (P?<? 0.05) between dogs infected with E. multilocularis from the four areas. None of the other independent variables was statistically significant. CONCLUSIONS:The results from this study indicate a high prevalence of both E. granulosus and E. muiltilocularis in dogs in Xiji County, NHAR. Transmission of E. multilocularis was more impacted by geographical risk-factors in Xiji County than that of E. granulosus. Dogs have the potential to maintain the transmission of both species of Echinococcus within local Xiji communities, and the current praziquantel dosing of dogs appears to be ineffective or poorly implemented in this area.

Dataset Information

Comprehensive characterization of plasma cell-free Echinococcus spp. DNA in echinococcosis patients using ultra-high-throughput sequencing.

Publications

Comprehensive characterization of plasma cell-free Echinococcus spp. DNA in echinococcosis patients using ultra-high-throughput sequencing.

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