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Naik B, Sasikumar J, Das SP. From Skin and Gut to the Brain: The Infectious Journey of the Human Commensal Fungus Malassezia and Its Neurological Consequences. Mol Neurobiol 2024:10.1007/s12035-024-04270-w. [PMID: 38871941 DOI: 10.1007/s12035-024-04270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
The human mycobiome encompasses diverse communities of fungal organisms residing within the body and has emerged as a critical player in shaping health and disease. While extensive research has focused on the skin and gut mycobiome, recent investigations have pointed toward the potential role of fungal organisms in neurological disorders. Among those fungal organisms, the presence of the commensal fungus Malassezia in the brain has created curiosity because of its commensal nature and primary association with the human skin and gut. This budding yeast is responsible for several diseases, such as Seborrheic dermatitis, Atopic dermatitis, Pityriasis versicolor, Malassezia folliculitis, dandruff, and others. However recent findings surprisingly show the presence of Malassezia DNA in the brain and have been linked to diseases like Alzheimer's disease, Parkinson's disease, Multiple sclerosis, and Amyotrophic lateral sclerosis. The exact role of Malassezia in these disorders is unknown, but its ability to infect human cells, travel through the bloodstream, cross the blood-brain barrier, and reside along with the lipid-rich neuronal cells are potential mechanisms responsible for pathogenesis. This also includes the induction of pro-inflammatory cytokines, disruption of the blood-brain barrier, gut-microbe interaction, and accumulation of metabolic changes in the brain environment. In this review, we discuss these key findings from studies linking Malassezia to neurological disorders, emphasizing the complex and multifaceted nature of these cases. Furthermore, we discuss potential mechanisms through which Malassezia might contribute to the development of neurological conditions. Future investigations will open up new avenues for our understanding of the fungal gut-brain axis and how it influences human behavior. Collaborative research efforts among microbiologists, neuroscientists, immunologists, and clinicians hold promise for unraveling the enigmatic connections between human commensal Malassezia and neurological disorders.
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Affiliation(s)
- Bharati Naik
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Jayaprakash Sasikumar
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Shankar Prasad Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
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Schlunck G, Maier P, Maier B, Maier W, Strempel S, Reinhard T, Heinzelmann S. Next-Generation Sequencing of the Human Aqueous Humour Microbiome. Int J Mol Sci 2024; 25:6128. [PMID: 38892316 PMCID: PMC11173048 DOI: 10.3390/ijms25116128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
The microbiome of the ocular surface has been characterised, but only limited information is available on a possible silent intraocular microbial colonisation in normal eyes. Therefore, we performed next-generation sequencing (NGS) of 16S rDNA genes in the aqueous humour. The aqueous humour was sampled from three patients during cataract surgery. Air swabs, conjunctival swabs from patients as well as from healthy donors served as controls. Following DNA extraction, the V3 and V4 hypervariable regions of the 16S rDNA gene were amplified and sequenced followed by denoising. The resulting Amplicon Sequence Variants were matched to a subset of the Ribosomal Database Project 16S database. The deduced bacterial community was then statistically analysed. The DNA content in all samples was low (0-1.49 ng/µL) but sufficient for analysis. The main phyla in the samples were Acinetobacteria (48%), Proteobacteria (26%), Firmicutes (14%), Acidobacteria (8%), and Bacteroidetes (2%). Patients' conjunctival control samples and anterior chamber fluid showed similar patterns of bacterial species containing many waterborne species. Non-disinfected samples showed a different bacterial spectrum than the air swab samples. The data confirm the existence of an ocular surface microbiome. Meanwhile, a distinct intraocular microbiome was not discernible from the background, suggesting the absence of an intraocular microbiome in normal eyes.
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Affiliation(s)
- Günther Schlunck
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg im Breisgau, Germany; (G.S.); (P.M.); (T.R.)
| | - Philip Maier
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg im Breisgau, Germany; (G.S.); (P.M.); (T.R.)
| | - Barbara Maier
- Institute for Infection Prevention and Control, Faculty of Medicine, University of Freiburg, 79110 Freiburg im Breisgau, Germany;
| | - Wolfgang Maier
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg im Breisgau, Germany;
| | | | - Thomas Reinhard
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg im Breisgau, Germany; (G.S.); (P.M.); (T.R.)
| | - Sonja Heinzelmann
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg im Breisgau, Germany; (G.S.); (P.M.); (T.R.)
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Bauer A, Hegen H, Reindl M. Body fluid markers for multiple sclerosis and differential diagnosis from atypical demyelinating disorders. Expert Rev Mol Diagn 2024; 24:283-297. [PMID: 38533708 DOI: 10.1080/14737159.2024.2334849] [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: 11/28/2023] [Accepted: 03/21/2024] [Indexed: 03/28/2024]
Abstract
INTRODUCTION Body fluid markers could be helpful to predict the conversion into clinically definite multiple sclerosis (MS) in people with a first demyelinating event of the central nervous system (CNS). Consequently, biomarkers such as oligoclonal bands, which are integrated in the current MS diagnostic criteria, could assist early MS diagnosis. AREAS COVERED This review examines existing knowledge on a broad spectrum of body fluid markers in people with a first CNS demyelinating event, explores their potential to predict conversion to MS, to assess MS disease activity, as well as their utility to differentiate MS from atypical demyelinating disorders such as neuromyelitis optica spectrum disorder and myelin oligodendrocyte glycoprotein associated disease. EXPERT OPINION This field of research has shown a dramatic increase of evidence, especially in the last decade. Some biomarkers are already established in clinical routine (e.g. oligoclonal bands) while others are currently implemented (e.g. kappa free light chains) or considered as breakthroughs (e.g. neurofilament light). Determination of biomarkers poses challenges for continuous monitoring, especially if exclusively detectable in cerebrospinal fluid. A handful of biomarkers are measurable in blood which holds a significant potential.
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Affiliation(s)
- Angelika Bauer
- Clinical Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Hegen
- Clinical Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Reindl
- Clinical Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
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Perlejewski K, Radkowski M, Pawełczyk A, Rydzanicz M, Dzieciątkowski T, Makowiecki M, Paciorek M, Welc-Falęciak R, Horban A, Laskus T. Enteroviral central nervous system infections in patients with Lyme neuroborreliosis. Ticks Tick Borne Dis 2023; 14:102253. [PMID: 37729847 DOI: 10.1016/j.ttbdis.2023.102253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/21/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
Patients with Lyme neuroborreliosis (LNB) are rarely tested for the presence of neurovirulent viruses other than tick-borne encephalitis virus (TBEV); however, such coinfections could be of clinical importance. The aim of the study was to search for the presence of neurotropic viruses in a LNB patients. Fourteen patients admitted with signs and symptoms of neuroinfection who were eventually diagnosed to have LNB (according to the guidelines of the European Federation of Neurological Societies) were subjects of the study. Sera and cerebrospinal fluid (CSF) collected at the time of initial presentation were tested for viral pathogens most common in our geographical area: human enteroviruses (EV), herpes simplex virus type 1 and 2, varicella-zoster virus, Epstein-Barr virus, cytomegalovirus, human herpesvirus type 6, human adenoviruses, and TBEV using PCR/RT-PCR and serological assays. RNA and DNA-based metagenomic next-generation sequencing (mNGS) was used to detect other viral pathogens. EV was detected in CSF from two (14 %) LNB patients and viral loads were similar (220 and 270 copies/ml). The mMGS analysis were performed on CSFs from 10 patients and generated a total 213,750,885 NGS reads, 0.05 % of which were viral. However, none of potential pathogens fulfilled the criteria for positive viral detection by mNGS. Using a number of PCR/RT-PCR assays and mNGS we identified EV infection in two out of 14 LNB patients. The possible co-occurrence of enterovirus and Lyme neuroborreliosis infections may warrant further research.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland.
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland
| | - Tomasz Dzieciątkowski
- Department of Microbiology, Medical University of Warsaw, Chalubińskiego 5, Warsaw 02-004, Poland
| | - Michał Makowiecki
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
| | - Marcin Paciorek
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
| | - Renata Welc-Falęciak
- Department of Parasitology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02-096, Poland
| | - Andrzej Horban
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
| | - Tomasz Laskus
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
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Dunalska A, Saramak K, Szejko N. The Role of Gut Microbiome in the Pathogenesis of Multiple Sclerosis and Related Disorders. Cells 2023; 12:1760. [PMID: 37443793 PMCID: PMC10341087 DOI: 10.3390/cells12131760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic, progressive neuroinflammatory disease with a complex pathophysiological background. A variety of diverse factors have been attributed to the propagation of inflammation and neurodegeneration in MS, mainly genetic, immunological, and environmental factors such as vitamin D deficiency, infections, or hormonal disbalance. Recently, the importance of the gut-brain axis for the development of many neurological conditions, including stroke, movement disorders, and neuroinflammatory disorders, has been postulated. The purpose of our paper was to summarize current evidence confirming the role of the gut microbiome in the pathophysiology of MS and related disorders, such as neuromyelitis optica spectrum disorder (NMO-SD). For this aim, we conducted a systematic review of the literature listed in the following databases: Medline, Pubmed, and Scopus, and were able to identify several studies demonstrating the involvement of the gut microbiome in the pathophysiology of MS and NMO-SD. It seems that the most relevant bacteria for the pathophysiology of MS are those belonging to Pseudomonas, Mycoplasma, Haemophilus, Blautia, Dorea, Faecalibacterium, Methanobrevibacter, Akkermansia, and Desulfovibrionaceae genera, while Clostridium perfringens and Streptoccocus have been demonstrated to play a role in the pathophysiology of NMO-SD. Following this line of evidence, there is also some preliminary data supporting the use of probiotics or other agents affecting the microbiome that could potentially have a beneficial effect on MS/NMO-SD symptoms and prognosis. The topic of the gut microbiome in the pathophysiology of MS is therefore relevant since it could be used as a biomarker of disease development and progression as well as a potential disease-modifying therapy.
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Affiliation(s)
- Anna Dunalska
- Department of Neurology, Medical University of Warsaw, 02-097 Warsaw, Poland;
| | - Kamila Saramak
- Department of Neurology, Hochzirl Hospital, 6170 Hochzirl, Austria;
| | - Natalia Szejko
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Bioethics, Medical University of Warsaw, 02-091 Warsaw, Poland
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Goswami K, Clarkson S, Tipton C, Phillips CD, Dennis DA, Klatt BA, O'Malley M, Smith EL, Gililland J, Pelt CE, Peters CL, Malkani AL, Palumbo BT, Lyons ST, Bernasek TL, Minter J, Goyal N, Purtill W, McDonald JF, Cross MB, Prieto HA, Lee GC, Hansen EN, Bini SA, Ward DT, Zhao N, Shohat N, Higuera CA, Nam D, Della Valle CJ, Parvizi J. The Microbiome of Osteoarthritic Hip and Knee Joints: A Prospective Multicenter Investigation. J Bone Joint Surg Am 2023; Publish Ahead of Print:00004623-990000000-00799. [PMID: 37192280 DOI: 10.2106/jbjs.22.00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
BACKGROUND Recent advances in high-throughput DNA sequencing technologies have made it possible to characterize the microbial profile in anatomical sites previously assumed to be sterile. We used this approach to explore the microbial composition within joints of osteoarthritic patients. METHODS This prospective multicenter study recruited 113 patients undergoing hip or knee arthroplasty between 2017 and 2019. Demographics and prior intra-articular injections were noted. Matched synovial fluid, tissue, and swab specimens were obtained and shipped to a centralized laboratory for testing. Following DNA extraction, microbial 16S-rRNA sequencing was performed. RESULTS Comparisons of paired specimens indicated that each was a comparable measure for microbiological sampling of the joint. Swab specimens were modestly different in bacterial composition from synovial fluid and tissue. The 5 most abundant genera were Escherichia, Cutibacterium, Staphylococcus, Acinetobacter, and Pseudomonas. Although sample size varied, the hospital of origin explained a significant portion (18.5%) of the variance in the microbial composition of the joint, and corticosteroid injection within 6 months before arthroplasty was associated with elevated abundance of several lineages. CONCLUSIONS The findings revealed that prior intra-articular injection and the operative hospital environment may influence the microbial composition of the joint. Furthermore, the most common species observed in this study were not among the most common in previous skin microbiome studies, suggesting that the microbial profiles detected are not likely explained solely by skin contamination. Further research is needed to determine the relationship between the hospital and a "closed" microbiome environment. These findings contribute to establishing the baseline microbial signal and identifying contributing variables in the osteoarthritic joint, which will be valuable as a comparator in the contexts of infection and long-term arthroplasty success. LEVEL OF EVIDENCE Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.
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Affiliation(s)
- Karan Goswami
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Samuel Clarkson
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Craig Tipton
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas
| | - Caleb D Phillips
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas
| | | | - Brian A Klatt
- Department of Orthopaedic Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Michael O'Malley
- Department of Orthopaedic Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Eric L Smith
- New England Baptist Hospital, Chestnut Hill, Massachusetts
| | - Jeremy Gililland
- Department of Orthopaedics, University of Utah, Salt Lake City, Utah
| | | | | | - Arthur L Malkani
- University of Louisville Adult Reconstruction Program, Louisville, Kentucky
| | - Brian T Palumbo
- University of South Florida Department of Orthopaedic Surgery, Clearwater, Florida
| | - Steven T Lyons
- University of South Florida Department of Orthopaedic Surgery, Clearwater, Florida
| | - Thomas L Bernasek
- University of South Florida Department of Orthopaedic Surgery, Clearwater, Florida
| | | | - Nitin Goyal
- Anderson Orthopaedic Research Institute, Alexandria, Virginia
| | - William Purtill
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | | | | | - Hernan A Prieto
- Department of Orthopaedics and Rehabilitation, University of Florida, Gainesville, Florida
| | - Gwo-Chin Lee
- Penn Presbyterian Medical Center, Philadelphia, Pennsylvania
| | - Erik N Hansen
- University of California San Francisco, San Francisco, California
| | - Stefano A Bini
- University of California San Francisco, San Francisco, California
| | - Derek T Ward
- University of California San Francisco, San Francisco, California
| | - Neil Zhao
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Noam Shohat
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Carlos A Higuera
- Department of Orthopaedic Surgery, Cleveland Clinic, Cleveland, Ohio
| | - Dennis Nam
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, Illinois
| | - Craig J Della Valle
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, Illinois
| | - Javad Parvizi
- Rothman Orthopaedic Institute, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
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Hao L, Wen P, Song W, Zhang B, Wu Y, Zhang Y, Ma T, Qiu Y. Direct detection and identification of periprosthetic joint infection pathogens by metagenomic next-generation sequencing. Sci Rep 2023; 13:7897. [PMID: 37193765 DOI: 10.1038/s41598-023-35215-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/15/2023] [Indexed: 05/18/2023] Open
Abstract
This study assessed the application of metagenomic next-generation sequencing in pathogen detection of periprosthetic joint infections. A total of 95 cases who previously had undergone hip and knee replacement undergoing revision from January 2018 to January 2021 were included in this study. Specimens of synovial fluid and deep-tissue were collected for culture and metagenomic next-generation sequencing, and patients were retrospectively categorized as infected or aseptic using the Musculoskeletal Infection Society criteria after revision surgery. The sensitivity, specificity, positive and negative predictive values were compared. A total of 36 cases had positive culture results and 59 cases had positive metagenomic next-generation sequencing results. Culture was positive in 34 infected cases (58.6%) and 2 aseptic cases (5.4%). Metagenomic next-generation sequencing was positive in 55 infected cases (94.8%) and 4 aseptic cases (10.8%). Five cases diagnosed with infection had other potential pathogens detected by metagenomic next-generation sequencing. Among the 24 culture-negative periprosthetic joint infections, metagenomic next-generation sequencing was able to identify potential pathogens in 21 cases (87.5%). From sampling to reporting, the average time needed for culture was 5.2 (95% CI 3.1-7.3) days, while that for metagenomic next-generation sequencing was 1.3 (95% CI 0.9-1.7) days. Metagenomic next-generation sequencing is more advantageous in pathogen detection of periprosthetic joint infection after total joint replacement, especially in patients with multiple infections or negative culture results.
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Affiliation(s)
- Linjie Hao
- Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Pengfei Wen
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Wei Song
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Binfei Zhang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Yanjie Wu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Yumin Zhang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China.
| | - Tao Ma
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China.
| | - Yusheng Qiu
- Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
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Chang Y, Jiang K, Zhang L, Yang F, Huang J. Application of next-generation sequencing technology in the detection of pathogenic bacteria of the periprosthetic joint infection after arthroplasty. Int Wound J 2023. [PMID: 36647902 DOI: 10.1111/iwj.14087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
To investigate the application value of next-generation sequencing (NGS) technology in the detection of pathogenic bacteria in the periprosthetic joint infection after arthroplasty. Twenty-two cases of patients with joint infection after arthroplasty in our hospital from March 2020 to March 2021 were selected, with 11 cases of knee and 11 cases of hip, including 8 cases of male and 14 cases of female, and an average age of 63.55 ± 13.11 years old (range from 28 to 85). Microbiological culture results of synovial fluid and periprosthetic joint tissue and NGS results of periprosthetic joint tissue were collected. The detection rate of NGS and microbiological culture were calculated and statistically analysed by paired χ2 test. Among the 22 patients with joint infection after arthroplasty, the positive rate of NGS was 90.91% (20/22), whereas the positive rate of bacterial culture was 50.00% (11/22). Paired chi-square test showed a statistically significant difference in the detection rate between the two groups (P = .0029). In the detection of pathogenic microorganism, NGS detected 12 kinds of bacteria, Staphylococcus aureus in 3 patients, Staphylococcus epidermidis in 5 cases, Streptococcus 1 case, Streptococcus dysgalactiae 1 case, Xanthomonas campestris 3 cases, Escherichia coli 2 cases, Bacillus cereus 2 cases, Klebsiella pneumoniae 1 case, Finegoldia magna 1 case, Corynebacterium klopensteriella in 1 case, Brucella 1 case, and Aspergillus flavus 1 case. Bacterial culture detected 6 kinds of bacteria, included 5 cases of Staphylococcus epidermis (including 3 cases of Methicillin-resistant coagulase-negative Staphylococcus, (MRSCoN)), 2 cases of Staphylococcus aureus (both Methicillin-resistant Staphylococcus aureus, (MRSA)), 1 case of Klebsiella pneumoniae, 1 case of Staphylococcus hominis (MRSCoN), 1 case of G+ bacillus, and 1 case of Brucella. Compared with bacterial culture, NGS technology has some advantages in the detection efficiency, detection rate, and comprehensiveness, which might be greater diagnostic value in the joint fluid of infection after arthroplasty.
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Affiliation(s)
- Yu Chang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Kai Jiang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Lixin Zhang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Fang Yang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Jing Huang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
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Guo Y, Yang Y, Xu M, Shi G, Zhou J, Zhang J, Li H. Trends and Developments in the Detection of Pathogens in Central Nervous System Infections: A Bibliometric Study. Front Cell Infect Microbiol 2022; 12:856845. [PMID: 35573778 PMCID: PMC9100591 DOI: 10.3389/fcimb.2022.856845] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/29/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction Rapid, sensitive, and specific laboratory assays are critical for the diagnosis and management of central nervous system (CNS) infections. The purpose of this study is to explore the intellectual landscape of research investigating methods for the detection of pathogens in patients with CNS infections and to identify the development trends and research frontier in this field. Methods A bibliometric study is conducted by analyzing literature retrieved from the Web of Science (WoS) Core Collection Database for the years 2000 to 2021. CiteSpace software is used for bibliometric analysis and network visualization, including co-citation analysis of references, co-occurrence analysis of keywords, and cooperation network analysis of authors, institutions, and countries/regions. Results A total of 2,282 publications are eventually screened, with an upward trend in the number of publications per year. The majority of papers are attributed to the disciplines of MICROBIOLOGY, INFECTIOUS DISEASES, IMMUNOLOGY, NEUROSCIENCES & NEUROLOGY, and VIROLOGY. The co-citation analysis of references shows that recent research has focused on the largest cluster “metagenomic next-generation sequencing”; the results of the analysis of the highest-cited publications and the citation burst of publications reveal that there is a strong interest stimulated in metagenomic next-generation sequencing. The co-occurrence analysis of keywords indicates that “infection”, “pathogen”, “diagnosis”, “gene”, “virus”, “polymerase chain reaction”, “cerebrospinal fluid”, “epidemiology”, and “metagenomic next-generation sequencing” are the main research priorities in the field of pathogen detection for CNS infections, and the keyword with the highest strength of burst is “metagenomic next-generation sequencing”. Collaborative network analysis reveals that the USA, the Centers for Disease Control and Prevention of USA, and XIN WANG and JENNIFER DIEN BARD are the most influential country, institution, and researchers, respectively. Conclusions Exploring more advanced laboratory assays to improve the diagnostic accuracy of pathogens is essential for CNS infection research. Metagenomic next-generation sequencing is emerging as a novel useful unbiased approach for diagnosing infectious diseases of the CNS.
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Affiliation(s)
- Yangyang Guo
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanlin Yang
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ming Xu
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guangzhi Shi
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jianxin Zhou
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jindong Zhang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- *Correspondence: Jindong Zhang, ; Hongliang Li,
| | - Hongliang Li
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Jindong Zhang, ; Hongliang Li,
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Jurasz H, Pawłowski T, Perlejewski K. Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives. Front Microbiol 2021; 12:745076. [PMID: 34745046 PMCID: PMC8564396 DOI: 10.3389/fmicb.2021.745076] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.
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Affiliation(s)
- Henryk Jurasz
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Pawłowski
- Division of Psychotherapy and Psychosomatic Medicine, Department of Psychiatry, Wrocław Medical University, Wrocław, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Dzieciątkowski T, Zakrzewska-Pniewska B, Podlecka-Piętowska A, Filipiak A, Barć K, Caraballo Cortés K, Pawełczyk A, Radkowski M, Laskus T. Search for viral agents in cerebrospinal fluid in patients with multiple sclerosis using real-time PCR and metagenomics. PLoS One 2020; 15:e0240601. [PMID: 33112911 PMCID: PMC7592794 DOI: 10.1371/journal.pone.0240601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic, immune-mediated demyelinating disease of the central nervous system of unclear etiology, but there is some evidence that viral infections could be responsible for triggering autoimmune mechanisms against myelin. We searched for viral RNA and DNA in cerebrospinal fluid (CSF) of 34 MS patients and 13 controls using RT-PCR/PCR against common neurotropic viruses. In addition, shotgun DNA- and RNA-based metagenomics were done in 13 MS patients and 4 controls. Specific quantitative real-time RT-PCR/PCR testing revealed the presence of viral nucleic acid in seven (20.59%) MS patients and in one (7.69%) control patient. In MS patients the most frequently detected was human herpesvirus type 6 (HHV-6; 3 cases; 8.82%); followed by Epstein-Barr virus (EBV; 2 cases; 5.88%), varicella zoster virus (VZV; 1 case; 2.94%) and Enterovirus (EV; 1 case; 2.94%). The single identified virus among controls was EBV (7.69%). DNA and RNA metagenomic assays did not identify any known eukaryotic viruses even though three of the analyzed samples were low-level positive by specific quantitative real-time PCR. In conclusion, we detected the presence of Herpesviridae and occasionally Enteroviridae in CSF from patients with MS but their prevalence was not significantly higher than among controls. Metagenomic analysis seems to be less sensitive than real-time RT-PCR/PCR and it did not detect any potential viral pathogens.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | | | | | - Agata Filipiak
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Barć
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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12
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A Collaborative Tale of Diagnosing and Treating Chronic Pulmonary Aspergillosis, from the Perspectives of Clinical Microbiologists, Surgical Pathologists, and Infectious Disease Clinicians. J Fungi (Basel) 2020; 6:jof6030106. [PMID: 32664547 PMCID: PMC7558816 DOI: 10.3390/jof6030106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic pulmonary aspergillosis (CPA) refers to a spectrum of Aspergillus-mediated disease that is associated with high morbidity and mortality, with its true prevalence vastly underestimated. The diagnosis of CPA includes characteristic radiographical findings in conjunction with persistent and systemic symptoms present for at least three months, and evidence of Aspergillus infection. Traditionally, Aspergillus infection has been confirmed through histopathology and microbiological studies, including fungal culture and serology, but these methodologies have limitations that are discussed in this review. The treatment of CPA requires an individualized approach and consideration of both medical and surgical options. Most Aspergillus species are considered susceptible to mold-active triazoles, echinocandins, and amphotericin B; however, antifungal resistance is emerging and well documented, demonstrating the need for novel therapies and antifungal susceptibility testing that correlates with clinical response. Here, we describe the clinical presentation, diagnosis, and treatment of CPA, with an emphasis on the strengths and pitfalls of diagnostic and treatment approaches, as well as future directions, including whole genome sequencing and metagenomic sequencing. The advancement of molecular technology enables rapid and precise species level identification, and the determination of molecular mechanisms of resistance, bridging the clinical infectious disease, anatomical pathology, microbiology, and molecular biology disciplines.
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13
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Ji XC, Zhou LF, Li CY, Shi YJ, Wu ML, Zhang Y, Fei XF, Zhao G. Reduction of Human DNA Contamination in Clinical Cerebrospinal Fluid Specimens Improves the Sensitivity of Metagenomic Next-Generation Sequencing. J Mol Neurosci 2020; 70:659-666. [PMID: 32002752 DOI: 10.1007/s12031-019-01472-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 12/26/2019] [Indexed: 12/25/2022]
Abstract
Metagenomics next-generation sequencing (mNGS) is increasingly available for the detection of obscure infectious diseases of the central nervous system. However, human DNA contamination from elevated white cells, one of the characteristic cerebrospinal fluid (CSF) features in meningitis patients, greatly reduces the sensitivity of mNGS in the pathogen detection. Currently, effective approaches to selectively reduce host DNA contamination from clinical CSF samples are still lacking. In this study, a total of 20 meningitis patients were enrolled, including 10 definitively diagnosed tuberculous meningitis (TBM) and 10 definite cryptococcal meningitis (CM) cases. To evaluate the effect of reduced human DNA in the sensitivity of mNGS detection, three specimen-processing protocols were performed: (i) To remove human DNA, saponin, a nonionic surfactant, was used to selectively lyse white cells in CSF followed by DNase treatment prior to the extraction of DNA; (ii) to reduce host DNA, CSF was centrifuged to remove human cells, and the supernatant was collected for DNA extraction; and (iii) DNA extraction from the unprocessed specimens was set as the control. We found that saponin processing significantly elevated the NGS unique reads for Cryptococcus (P < 0.01) compared with the control but had no effects for Mycobacterium tuberculosis (P > 0.05). However, detection of centrifuged supernatants improved the NGS unique reads for both TBM and CM compared with controls (P < 0.01). Our results demonstrate that the use of mNGS of centrifuged supernatants from clinical CSF samples in patients with TBM and CM is a simple and effective method to improve the sensitivity of pathogen detection.
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MESH Headings
- Adult
- Aged
- Cerebrospinal Fluid/microbiology
- Cryptococcus/genetics
- Cryptococcus/pathogenicity
- Female
- Genome, Bacterial
- Genome, Human
- High-Throughput Nucleotide Sequencing/methods
- High-Throughput Nucleotide Sequencing/standards
- Humans
- Male
- Meningitis, Cryptococcal/cerebrospinal fluid
- Meningitis, Cryptococcal/diagnosis
- Meningitis, Cryptococcal/microbiology
- Metagenomics/methods
- Metagenomics/standards
- Middle Aged
- Molecular Diagnostic Techniques/methods
- Molecular Diagnostic Techniques/standards
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/pathogenicity
- Sensitivity and Specificity
- Sequence Analysis, DNA/methods
- Sequence Analysis, DNA/standards
- Tuberculosis, Meningeal/cerebrospinal fluid
- Tuberculosis, Meningeal/diagnosis
- Tuberculosis, Meningeal/microbiology
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Affiliation(s)
- Xin-Chao Ji
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Lin-Fu Zhou
- Department of Neurology, The 987 Hospital of PLA, Baoji, China
| | - Chao-Yang Li
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Ya-Jun Shi
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Meng-Li Wu
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Yun Zhang
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Xiao-Fei Fei
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Gang Zhao
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China.
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Tiew PY, Mac Aogain M, Ali NABM, Thng KX, Goh K, Lau KJX, Chotirmall SH. The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges. Mycopathologia 2020; 185:207-231. [PMID: 31894501 PMCID: PMC7223441 DOI: 10.1007/s11046-019-00413-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Micheál Mac Aogain
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | | | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Karlyn Goh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kenny J X Lau
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.
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15
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Ordoñez G, Rivas V, Santos M, Mondragon M, Pineda B, Rodríguez K, Corona T, Flores J, Sotelo J. Herpes viruses in optic neuritis: Similar to Bell’s palsy. Clin Neurol Neurosurg 2020; 188:105588. [DOI: 10.1016/j.clineuro.2019.105588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/03/2019] [Indexed: 11/27/2022]
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16
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Thoendel MJ, Jeraldo PR, Greenwood-Quaintance KE, Yao JZ, Chia N, Hanssen AD, Abdel MP, Patel R. Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach. Clin Infect Dis 2019; 67:1333-1338. [PMID: 29648630 DOI: 10.1093/cid/ciy303] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/09/2018] [Indexed: 12/14/2022] Open
Abstract
Background Metagenomic shotgun sequencing has the potential to change how many infections, particularly those caused by difficult-to-culture organisms, are diagnosed. Metagenomics was used to investigate prosthetic joint infections (PJIs), where pathogen detection can be challenging. Methods Four hundred eight sonicate fluid samples generated from resected hip and knee arthroplasties were tested, including 213 from subjects with infections and 195 from subjects without infection. Samples were enriched for microbial DNA using the MolYsis basic kit, whole-genome amplified, and sequenced using Illumina HiSeq 2500 instruments. A pipeline was designed to screen out human reads and analyze remaining sequences for microbial content using the Livermore Metagenomics Analysis Toolkit and MetaPhlAn2 tools. Results When compared to sonicate fluid culture, metagenomics was able to identify known pathogens in 94.8% (109/115) of culture-positive PJIs, with additional potential pathogens detected in 9.6% (11/115). New potential pathogens were detected in 43.9% (43/98) of culture-negative PJIs, 21 of which had no other positive culture sources from which these microorganisms had been detected. Detection of microorganisms in samples from uninfected aseptic failure cases was conversely rare (7/195 [3.6%] cases). The presence of human and contaminant microbial DNA from reagents was a challenge, as previously reported. Conclusions Metagenomic shotgun sequencing is a powerful tool to identify a wide range of PJI pathogens, including difficult-to-detect pathogens in culture-negative infections.
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Affiliation(s)
- Matthew J Thoendel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Janet Z Yao
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Nicholas Chia
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Arlen D Hanssen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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17
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Chen MF, Chang CH, Chiang-Ni C, Hsieh PH, Shih HN, Ueng SWN, Chang Y. Rapid analysis of bacterial composition in prosthetic joint infection by 16S rRNA metagenomic sequencing. Bone Joint Res 2019; 8:367-377. [PMID: 31537994 PMCID: PMC6719533 DOI: 10.1302/2046-3758.88.bjr-2019-0003.r2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Objectives Prosthetic joint infection (PJI) is the most common cause of arthroplasty failure. However, infection is often difficult to detect by conventional bacterial cultures, for which false-negative rates are 23% to 35%. In contrast, 16S rRNA metagenomics has been shown to quantitatively detect unculturable, unsuspected, and unviable pathogens. In this study, we investigated the use of 16S rRNA metagenomics for detection of bacterial pathogens in synovial fluid (SF) from patients with hip or knee PJI. Methods We analyzed the bacterial composition of 22 SF samples collected from 11 patients with PJIs (first- and second-stage surgery). The V3 and V4 region of bacteria was assessed by comparing the taxonomic distribution of the 16S rDNA amplicons with microbiome sequencing analysis. We also compared the results of bacterial detection from different methods including 16S metagenomics, traditional cultures, and targeted Sanger sequencing. Results Polymicrobial infections were not only detected, but also characterized at different timepoints corresponding to first- and second-stage exchange arthroplasty. Similar taxonomic distributions were obtained by matching sequence data against SILVA, Greengenes, and The National Center for Biotechnology Information (NCBI). All bacteria isolated from the traditional culture could be further identified by 16S metagenomics and targeted Sanger sequencing. Conclusion The data highlight 16S rRNA metagenomics as a suitable and promising method to detect and identify infecting bacteria, most of which may be uncultivable. Importantly, the method dramatically reduces turnaround time to two days rather than approximately one week for conventional cultures. Cite this article: M-F. Chen, C-H. Chang, C. Chiang-Ni, P-H. Hsieh, H-N. Shih, S. W. N. Ueng, Y. Chang. Rapid analysis of bacterial composition in prosthetic joint infection by 16S rRNA metagenomic sequencing. Bone Joint Res 2019;8:367–377. DOI: 10.1302/2046-3758.88.BJR-2019-0003.R2.
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Affiliation(s)
- Mei-Feng Chen
- Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chih-Hsiang Chang
- Bone and Joint Research Center, Chang Gung Memorial Hospital; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital; Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University. Taoyuan, Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital. Taoyuan, Taiwan
| | - Pang-Hsin Hsieh
- Bone and Joint Research Center, Chang Gung Memorial Hospital; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsin-Nung Shih
- Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Steve W N Ueng
- Bone and Joint Research Center, Chang Gung Memorial Hospital; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuhan Chang
- Bone and Joint Research Center, Chang Gung Memorial Hospital; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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18
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Martí JM. Recentrifuge: Robust comparative analysis and contamination removal for metagenomics. PLoS Comput Biol 2019; 15:e1006967. [PMID: 30958827 PMCID: PMC6472834 DOI: 10.1371/journal.pcbi.1006967] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 04/18/2019] [Accepted: 03/19/2019] [Indexed: 12/21/2022] Open
Abstract
Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics.
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Affiliation(s)
- Jose Manuel Martí
- Institute for Integrative Systems Biology (ISysBio), Valencia, Spain
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19
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Forbes JD, Bernstein CN, Tremlett H, Van Domselaar G, Knox NC. A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease? Front Microbiol 2019; 9:3249. [PMID: 30687254 PMCID: PMC6333682 DOI: 10.3389/fmicb.2018.03249] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/14/2018] [Indexed: 02/05/2023] Open
Abstract
The human microbiome has received decades of attention from scientific and medical research communities. The human gastrointestinal tract is host to immense populations of microorganisms including bacteria, viruses, archaea, and fungi (the gut microbiota). High-throughput sequencing and computational advancements provide unprecedented ability to investigate the structure and function of microbial communities associated with the human body in health and disease. Most research to date has largely focused on elucidating the bacterial component of the human gut microbiota. Study of the gut "mycobiota," which refers to the diverse array of fungal species, is a relatively new and rapidly progressing field. Though omnipresent, the number and abundance of fungi occupying the human gut is orders of magnitude smaller than that of bacteria. Recent insights however, have suggested that the gut mycobiota may be intricately linked to health and disease. Evaluation of the gut mycobiota has shown that not only are the fungal communities altered in disease, but they also play a role in maintaining intestinal homeostasis and influencing systemic immunity. In addition, it is now widely accepted that host-fungi and bacteria-fungi associations are critical to host health. While research of the gut mycobiota in health and disease is on the rise, little research has been performed in the context of neuroimmune and neurodegenerative conditions. Gut microbiota dysbiosis (specifically bacteria and archaea) have been reported in neurological diseases such as multiple sclerosis, amyotrophic lateral sclerosis, and Alzheimer's, among others. Given the widely accepted bacteria-fungi associations and paucity of mycobiota-specific studies in neurological disease, this review discusses the potential role fungi may play in multiple sclerosis and other neurological diseases. Herein, we provide an overview of recent advances in gut mycobiome research and discuss the plausible role of both intestinal and non-intestinal fungi in the context of neuroimmune and neurodegenerative conditions.
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Affiliation(s)
- Jessica D. Forbes
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Charles N. Bernstein
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Helen Tremlett
- Centre for Brain Health and Faculty of Medicine (Neurology), University of British Columbia, Vancouver, BC, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Natalie C. Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
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20
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Mentis AFA, Dardiotis E, Grigoriadis N, Petinaki E, Hadjigeorgiou GM. Viruses and Multiple Sclerosis: From Mechanisms and Pathways to Translational Research Opportunities. Mol Neurobiol 2017; 54:3911-3923. [PMID: 28455696 DOI: 10.1007/s12035-017-0530-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/06/2017] [Indexed: 12/26/2022]
Abstract
Viruses are directly or indirectly implicated in multiple sclerosis (MS). Here, we review the evidence on the virus-related pathophysiology of MS, introduce common experimental models, and explore the ways in which viruses cause demyelination. By emphasizing knowledge gaps, we highlight future research directions for effective MS diagnostics and therapies: (i) identifying biomarkers for at-risk individuals, (ii) searching for direct evidence of specific causative viruses, (iii) establishing the contribution of host genetic factors and viruses, and (iv) investigating the contribution of immune regulation at extra-CNS sites. Research in these areas is likely to be facilitated by the application of high-throughput technologies, the development of systems-based bioinformatic approaches, careful selection of experimental models, and the acquisition of high-quality clinical material for tissue-based research.
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Affiliation(s)
- Alexios-Fotios A Mentis
- Department of Microbiology, University Hospital of Larissa, University of Thessaly, Larissa, Greece. .,The Johns Hopkins University, AAP, Baltimore, MD, USA.
| | - Efthimios Dardiotis
- Department of Neurology, University Hospital of Larissa, University of Thessaly, Larissa, Greece
| | - Nikolaos Grigoriadis
- B' Department of Neurology, Laboratory of Experimental Neurology and Neuroimmunology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Efthimia Petinaki
- Department of Microbiology, University Hospital of Larissa, University of Thessaly, Larissa, Greece
| | - Georgios M Hadjigeorgiou
- Department of Neurology, University Hospital of Larissa, University of Thessaly, Larissa, Greece
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21
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Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis. J Clin Microbiol 2017; 55:1789-1801. [PMID: 28356418 DOI: 10.1128/jcm.02402-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/17/2017] [Indexed: 01/24/2023] Open
Abstract
Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. Depending on the application, background DNA from WGA kits can be problematic. Three WGA kits were tested for their utility in a metagenomics approach to identify the pathogens in sonicate fluid comprised of biofilms and other materials dislodged from the surfaces of explanted prosthetic joints using sonication. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples. Variations in the number of background reads, the genera identified in the background, and the number of reads from known pathogens known to be present in the samples were observed between kits. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA. This approach also resulted in the presence of contaminant bacterial DNA and yielded fewer reads from the known pathogens. These findings highlight the impact that WGA kit selection can have on metagenomic analysis of low-biomass samples and the importance of the careful selection and consideration of the implications of using these tools.
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22
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Tremlett H, Bauer KC, Appel-Cresswell S, Finlay BB, Waubant E. The gut microbiome in human neurological disease: A review. Ann Neurol 2017; 81:369-382. [DOI: 10.1002/ana.24901] [Citation(s) in RCA: 315] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/17/2017] [Accepted: 02/17/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Helen Tremlett
- Faculty of Medicine (Neurology) and the Djavad Mowafaghian Centre for Brain Health; University of British Columbia; Vancouver British Columbia Canada
| | - Kylynda C. Bauer
- Microbiology and Immunology, Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
- Biochemistry and Molecular Biology; University of British Columbia; Vancouver British Columbia Canada
| | - Silke Appel-Cresswell
- Faculty of Medicine (Neurology) and the Djavad Mowafaghian Centre for Brain Health; University of British Columbia; Vancouver British Columbia Canada
- Pacific Parkinson's Research Centre; University of British Columbia; Vancouver British Columbia Canada
| | - Brett B. Finlay
- Microbiology and Immunology, Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
- Biochemistry and Molecular Biology; University of British Columbia; Vancouver British Columbia Canada
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