1
|
Scarsella E, Meineri G, Sandri M, Ganz HH, Stefanon B. Characterization of the Blood Microbiome and Comparison with the Fecal Microbiome in Healthy Dogs and Dogs with Gastrointestinal Disease. Vet Sci 2023; 10:vetsci10040277. [PMID: 37104432 PMCID: PMC10144428 DOI: 10.3390/vetsci10040277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/25/2023] [Accepted: 04/04/2023] [Indexed: 04/28/2023] Open
Abstract
Recent studies have found bacterial DNA in the blood of healthy individuals. To date, most studies on the blood microbiome have focused on human health, but this topic is an expanding research area in animal health as well. This study aims to characterize the blood microbiome of both healthy dogs and those with chronic gastro-enteropathies. For this study, blood and fecal samples were collected from 18 healthy and 19 sick subjects, DNA was extracted through commercial kits, and the V3-V4 regions of the 16S rRNA gene were sequenced on the Illumina platform. The sequences were analyzed for taxonomic annotation and statistical analysis. Alpha and beta diversities of fecal microbiome were significantly different between the two groups of dogs. Principal coordinates analysis revealed that healthy and sick subjects were significantly clustered for both blood and fecal microbiome samples. Moreover, bacterial translocation from the gut to the bloodstream has been suggested because of found shared taxa. Further studies are needed to determine the origin of the blood microbiome and the bacteria viability. The characterization of a blood core microbiome in healthy dogs has potential for use as a diagnostic tool to monitor for the development of gastro-intestinal disease.
Collapse
Affiliation(s)
- Elisa Scarsella
- AnimalBiome, 400 29th Street, Suite 101, Oakland, CA 94609, USA
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Giorgia Meineri
- Department of Veterinary Science, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Misa Sandri
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Holly H Ganz
- AnimalBiome, 400 29th Street, Suite 101, Oakland, CA 94609, USA
| | - Bruno Stefanon
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| |
Collapse
|
2
|
Li X, Yang L, Li D, Yang X, Wang Z, Chen M, Wu F, Dou X, Niu M, Qi H, Deng T, Xia H, Wang D. Diagnosis of Neurological Infections in Pediatric Patients from Cell-Free DNA Specimens by Using Metagenomic Next-Generation Sequencing. Microbiol Spectr 2023; 11:e0253022. [PMID: 36651744 PMCID: PMC9927296 DOI: 10.1128/spectrum.02530-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
Central nervous system (CNS) infections can cause significant morbidity and mortality, especially in children. Rapid and accurate pathogenic detection in suspected CNS infections is essential for disease control at the early stage of infection. To evaluate the performance of metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) in pediatric patients, we retrospectively analyzed the efficiency of cfDNA mNGS in children with CNS infections (n = 257) or noninfectious neurological disorders (n = 81). The CSF samples of 124 random subjects were used to evaluate the accuracy between mNGS of cfDNA and whole-cell DNA (wcDNA). In total, cfDNA mNGS detected a wide range of microbes with a detection rate of 71.0%, and the sensitivity and total coincidence rate with clinical diagnosis reached 68.9% and 67.5%, respectively. Compared with wcDNA mNGS, cfDNA mNGS had a higher efficacy in detecting viruses (66 versus 13) and Mycobacterium (7 versus 1), with significantly higher reads per million. The dominant causative pathogens were bacteria and viruses in CNS infections, but these presented with different pathogen spectra in different age categories. The best timing for the mNGS test ranged from 1 to 6 days after the start of anti-infection therapy, and the earlier mNGS started, the better was identification of bacterial CNS infections. This study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in pediatric CNS infections, and it was even better than wcDNA mNGS. Furthermore, research needs to be better validated in large-scale clinical trials to improve the clinical applications of cfDNA mNGS. IMPORTANCE Our study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in CNS-infected children, and it was even better than wcDNA mNGS. cfDNA mNGS detected a wide range of pathogens with a high total coincidence rate (67.5%) against clinical diagnosis. The best timing for cfDNA mNGS detection ranged from 1 to 6 days, rather than 0 days, after the start of empirical anti-infection therapy. The earlier mNGS started, the better the identifications of bacterial CNS infections. To the best of our knowledge, this research is the first report evaluating the clinical utility of mNGS with different methods (cfDNA versus wcDNA) of extracting DNA from CSF specimens in diagnosing pediatric CNS infections. Meanwhile, this is the largest cohort study that has evaluated the performance of mNGS using cfDNA from CSF specimens in pediatric patients with CNS infections.
Collapse
Affiliation(s)
- Xia Li
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Le Yang
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Dongjing Li
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Xuying Yang
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Zhijing Wang
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Mengyi Chen
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Fang Wu
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Xiangjun Dou
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Mengmeng Niu
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - HongYan Qi
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Ting Deng
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Han Xia
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Dong Wang
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| |
Collapse
|
3
|
Goraya MU, Li R, Mannan A, Gu L, Deng H, Wang G. Human circulating bacteria and dysbiosis in non-infectious diseases. Front Cell Infect Microbiol 2022; 12:932702. [PMID: 36093202 PMCID: PMC9448904 DOI: 10.3389/fcimb.2022.932702] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/01/2022] [Indexed: 02/05/2023] Open
Abstract
Blood microorganisms were once thought to indicate infection. Blood in healthy people appears to be devoid of growing bacteria; nonetheless, intracellular dormant forms of bacteria have been reported previously. With breakthroughs in sequencing and bioinformatics, the presence of bacterial DNA in healthy human blood initiated the controversy of human blood microbiota (HBM). Recently, bacteria-specific DNA and culturable bacteria were found in healthy human blood. Researchers wanted to study the phenomena of a "healthy blood microbiota" by providing a thorough description of bacterially produced nucleic acids using many complementing molecular and traditional microbiological approaches. Because blood is a relatively limited and particular environment, culturability and plate count issues can be overcome using enhanced cultured procedures. However, more evidence is required to confirm that healthy human blood contains normal microbiota. Cavities, mouth and intestinal microbiota, trauma, surgery, and animal/insect bites can introduce bacteria into human blood. All these factors strengthen the concept of transient blood bacteria too. The presence of blood bacteria may be caused by temporary immunological clearance and absorption by dendritic or M cells. This review provides an extensive and comprehensive analysis that suggests that healthy blood bacteria may not be typical microbiota but transient circulatory microorganisms. In this study, we look at how contaminants (Escherichia, Shigella, Pseudomonads, etc.) from the skin, laboratory environments, and reagents can affect the interpretation of blood-derived microbial information and the relationship between the circulating bacteria and non-communicable diseases. Circulating transient bacteria may play a role in the pathogenesis of non-infectious diseases such as diabetes and CVD. Contamination-free hematological studies can aid in understanding the disease mechanisms, therapy, and biomarkers.
Collapse
Affiliation(s)
- Mohsan Ullah Goraya
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Rui Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Abdul Mannan
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
| | - Liming Gu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Huixiong Deng
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Gefei Wang
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| |
Collapse
|
4
|
Wang L, Li F, Gu B, Qu P, Liu Q, Wang J, Tang J, Cai S, Zhao Q, Ming Z. Metaomics in Clinical Laboratory: Potential Driving Force for Innovative Disease Diagnosis. Front Microbiol 2022; 13:883734. [PMID: 35783436 PMCID: PMC9247514 DOI: 10.3389/fmicb.2022.883734] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Currently, more and more studies suggested that reductionism was lack of holistic and integrative view of biological processes, leading to limited understanding of complex systems like microbiota and the associated diseases. In fact, microbes are rarely present in individuals but normally live in complex multispecies communities. With the recent development of a variety of metaomics techniques, microbes could be dissected dynamically in both temporal and spatial scales. Therefore, in-depth understanding of human microbiome from different aspects such as genomes, transcriptomes, proteomes, and metabolomes could provide novel insights into their functional roles, which also holds the potential in making them diagnostic biomarkers in many human diseases, though there is still a huge gap to fill for the purpose. In this mini-review, we went through the frontlines of the metaomics techniques and explored their potential applications in clinical diagnoses of human diseases, e.g., infectious diseases, through which we concluded that novel diagnostic methods based on human microbiomes shall be achieved in the near future, while the limitations of these techniques such as standard procedures and computational challenges for rapid and accurate analysis of metaomics data in clinical settings were also examined.
Collapse
Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Fen Li
- Department of Laboratory Medicine, Huaiyin Hospital, Huai’an, China
| | - Bin Gu
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Pengfei Qu
- The First School of Clinical Medicine, Xuzhou Medical University, Xuzhou, China
| | - Qinghua Liu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Junjiao Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Jiawei Tang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Shubin Cai
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, China
- *Correspondence: Qi Zhao,
| | - Zhong Ming
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
- Zhong Ming,
| |
Collapse
|
5
|
Zhang X, Feng P, Meng P, Li D, Gao H, Zhao Y, Yuan J, Wang Y, Xia H. Case Report: Severe Listeria Encephalitis With Complicated or Secondary Autoimmune Encephalitis and CNS Demyelinating Diseases. Front Public Health 2022; 10:848868. [PMID: 35646766 PMCID: PMC9133549 DOI: 10.3389/fpubh.2022.848868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/24/2022] [Indexed: 12/02/2022] Open
Abstract
Background Listeria monocytogenes is an important food-borne bacterium. It rarely infects patients with complete immunity and causes meningocephalitis. Patients with severe Listeria encephalitis always experience a bad prognosis. Case Presentation A 39-year-old male patient was admitted to our hospital due to fever for more than 10 days and disturbance of consciousness accompanied by convulsions for 2 days. Metagenomic next-generation sequencing (mNGS) results showed L. monocytogenes in both cerebrospinal fluid (CSF) and blood, indicating L. monocytogenes encephalitis. Autoimmune encephalitis and central nervous system (CNS) demyelinating autoantibodies in the CSF also showed positive results. The case was finally diagnosed as severe Listeria encephalitis with complicated or secondary autoimmune encephalitis and CNS demyelinating diseases. Conclusions It is necessary to carry out infection and immunity screening in patients with severe encephalitis, especially for immunocompromised patients. mNGS plays a pivotal role in screening patients with severe and difficult neurological diseases.
Collapse
Affiliation(s)
- Xiaomin Zhang
- Department of Neurology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Peng Feng
- Department of Neurology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Pengfei Meng
- Department of Neurology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Dongfang Li
- Department of Neurology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Huizhong Gao
- Department of Neurology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yang Zhao
- Department of Neurology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jingjing Yuan
- Acupuncture Hospital of Shanxi Province, Taiyuan, China
| | - Yongqing Wang
- Department of Neurology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Han Xia
- Hugobiotech Co., Ltd., Department of Scientific Affairs, Beijing, China
| |
Collapse
|