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Abdelrahman KN, Abdel Ghany AGA, Saber RA, Osman A, Sitohy B, Sitohy M. Anthocyanins from pomegranate peel ( Punica granatum), chili pepper fruit ( Capsicum annuum), and bougainvillea flowers ( Bougainvillea spectabilis) with multiple biofunctions: Antibacterial, antioxidant, and anticancer. Heliyon 2024; 10:e32222. [PMID: 38868073 PMCID: PMC11168436 DOI: 10.1016/j.heliyon.2024.e32222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
Background Natural colorants, including natural pigments, e.g., anthocyanins, carotenoids, and chlorophylls, in novel and attractive food matrixes have become a popular trend. They impart favorite colors to food products and provide significant therapeutic effects. This study is aimed at extracting and identifying some natural pigments from different plant sources and evaluating their ability as antibacterial, antioxidant, and anticancer activities. Methods The anthocyanin-rich extract (ARE) is derived from three natural plant sources: pomegranate peel (Punica granatum), chili pepper fruit (Capsicum annuum), and Bougainvillea flowers. Bougainvillea spectabilis are analyzed for biochemical composition, as well as antioxidant, antibacterial, and anticancer activity, HPLC, DPPH, FRAP, disc diffusion assay, MIC, MTT, VEGFR-2, and caspase-9 assays. Results All three extracts had varying total phenolic contents, ranging from 14 to 466 mg GAE/g extract, where Punica granatum was the highest (466 mg GAE/g extract), followed by Bougainvillea spectabilis (180 mg GAE/g extract), and then Capsicum annuum (14 mg GAE/g extract). The antioxidant activity rose steadily with raising concentration. The ARE of pomegranate peels recorded highest value, followed by Bougainvillea flowers and chili pepper fruit. The MTT assay revealed an inhibitory action of the tested extracts on the proliferation of HCT-116, MCF-7, and HepG2 in a concentration-based manner. Gene expression of caspase-9 transcripts was considerably multiplied by the application of ARE of pomegranate peels. All the tested extracts inhibited VEGFR-2, and the inhibition (%) expanded gradually with increasing concentrations, achieving the highest value (80 %) at 10 μg/mL. The ARE of pomegranate peels scored highest antibacterial activity, followed by ARE of chili pepper fruit and Bougainvillea flowers. The inhibition zone diameter escalated gradually with rising concentrations of the tested samples. Conclusion The AREs of the three studied plant sources can be used as multifunctional products with antioxidant, anticancer, and antibacterial activities that are natural, safe, and cheap.
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Affiliation(s)
| | | | - Refaat A. Saber
- Faculty of Development and Technology, Zagazig University, Zagazig, 44519, Egypt
| | - Ali Osman
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt
| | - Basel Sitohy
- Department of Clinical Microbiology, Infection, and Immunology, Umeå University, SE-90185, Umeå, Sweden
- Institution of Diagnostics and Intervention, Oncology, Umeå University, SE-90185, Umeå, Sweden
| | - Mahmoud Sitohy
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024:1-14. [PMID: 38772736 DOI: 10.1631/jzus.b2300029] [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: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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Yuan L, Zhu Q, Chen Q, Lai LM, Liu P, Liu Y. The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with infectious diseases. Lab Med 2024; 55:132-139. [PMID: 37289931 DOI: 10.1093/labmed/lmad046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVE Metagenomic next-generation sequencing (mNGS) can be used to detect pathogens in clinical infectious diseases through the sequencing analysis of microbial and host nucleic acids in clinical samples. This study aimed to assess the diagnostic performance of mNGS in patients with infections. METHODS In this study, 641 patients with infectious diseases were enrolled. These patients simultaneously underwent pathogen detection by both mNGS and microbial culture. Through statistical analysis, we judged the diagnostic performance of mNGS and microbial culture on different pathogens. RESULTS Among 641 patients, 276 cases of bacteria and 95 cases of fungi were detected by mNGS, whereas 108 cases of bacteria and 41 cases of fungi were detected by traditional cultures. Among all mixed infections, combined bacterial and viral infections were the highest (51%, 87/169), followed by combined bacterial with fungal infections (16.57%, 28/169) and mixed bacterial, fungal, and viral infections (13.61%, 23/169). Among all sample types, bronchoalveolar lavage fluid (BALF) samples had the highest positive rate (87.8%, 144/164), followed by sputum (85.4%, 76/89) and blood samples (61.2%, 158/258). For the culture method, sputum samples had the highest positive rate (47.2%, 42/89), followed by BALF (37.2%, 61/164). The positive rate of mNGS was 69.89% (448/641), which was significantly higher than that of traditional cultures (22.31% [143/641]) (P < .05). CONCLUSIONS Our results show that mNGS is an effective tool for the rapid diagnosis of infectious diseases. Compared with traditional detection methods, mNGS also showed obvious advantages in mixed infections and infections with uncommon pathogens.
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Affiliation(s)
- Lei Yuan
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qing Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Lan Min Lai
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Peng Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Moragues-Solanas L, Le-Viet T, McSorley E, Halford C, Lockhart DS, Aydin A, Kay GL, Elumogo N, Mullen W, O'Grady J, Gilmour MW. Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection. BMC Med Genomics 2024; 17:71. [PMID: 38443925 PMCID: PMC10916079 DOI: 10.1186/s12920-024-01835-5] [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: 11/17/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND The timely and accurate diagnosis of bloodstream infection (BSI) is critical for patient management. With longstanding challenges for routine blood culture, metagenomics is a promising approach to rapidly provide sequence-based detection and characterisation of bloodborne bacteria. Long-read sequencing technologies have successfully supported the use of clinical metagenomics for syndromes such as respiratory illness, and modified approaches may address two requisite factors for metagenomics to be used as a BSI diagnostic: depletion of the high level of host DNA to then detect the low abundance of microbes in blood. METHODS Blood samples from healthy donors were spiked with different concentrations of four prevalent causative species of BSI. All samples were then subjected to a modified saponin-based host DNA depletion protocol and optimised DNA extraction, whole genome amplification and debranching steps in preparation for sequencing, followed by bioinformatical analyses. Two related variants of the protocol are presented: 1mL of blood processed without bacterial enrichment, and 5mL of blood processed following a rapid bacterial enrichment protocol-SepsiPURE. RESULTS After first identifying that a large proportion of host mitochondrial DNA remained, the host depletion process was optimised by increasing saponin concentration to 3% and scaling the reaction to allow more sample volume. Compared to non-depleted controls, the 3% saponin-based depletion protocol reduced the presence of host chromosomal and mitochondrial DNA < 106 and < 103 fold respectively. When the modified depletion method was further combined with a rapid bacterial enrichment method (SepsiPURE; with 5mL blood samples) the depletion of mitochondrial DNA improved by a further > 10X while also increasing detectable bacteria by > 10X. Parameters during DNA extraction, whole genome amplification and long-read sequencing were also adjusted, and subsequently amplicons were detected for each input bacterial species at each of the spiked concentrations, ranging from 50-100 colony forming units (CFU)/mL to 1-5 CFU/mL. CONCLUSION In this proof-of-concept study, four prevalent BSI causative species were detected in under 12 h to species level (with antimicrobial resistance determinants) at concentrations relevant to clinical blood samples. The use of a rapid and precise metagenomic protocols has the potential to advance the diagnosis of BSI.
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Affiliation(s)
- Lluis Moragues-Solanas
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- University of East Anglia, Norwich, Norfolk, UK
| | - Thanh Le-Viet
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
| | - Elinor McSorley
- Momentum Bioscience Ltd, Blenheim Office Park, Witney, Oxfordshire, UK
| | - Carl Halford
- University of East Anglia, Norwich, Norfolk, UK
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, UK
| | - Daniel S Lockhart
- Momentum Bioscience Ltd, Blenheim Office Park, Witney, Oxfordshire, UK
| | - Alp Aydin
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- Oxford Nanopore Technologies Plc, Quadram Institute Bioscience, Norwich, UK
| | - Gemma L Kay
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- Oxford Nanopore Technologies Plc, Quadram Institute Bioscience, Norwich, UK
| | - Ngozi Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, UK
| | - William Mullen
- Momentum Bioscience Ltd, Blenheim Office Park, Witney, Oxfordshire, UK
| | - Justin O'Grady
- University of East Anglia, Norwich, Norfolk, UK
- Oxford Nanopore Technologies Plc, Quadram Institute Bioscience, Norwich, UK
| | - Matthew W Gilmour
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK.
- University of East Anglia, Norwich, Norfolk, UK.
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5
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Lin BW, Hong JC, Jiang ZJ, Zhang WQ, Fan QC, Yao XP. Performance of metagenomic next-generation sequencing in cerebrospinal fluid for diagnosis of tuberculous meningitis. J Med Microbiol 2024; 73. [PMID: 38506717 DOI: 10.1099/jmm.0.001818] [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] [Indexed: 03/21/2024] Open
Abstract
Purpose. Metagenomic next-generation sequencing (mNGS) has been widely used in the diagnosis of infectious diseases, while its performance in diagnosis of tuberculous meningitis (TBM) is incompletely characterized. The aim of this study was to assess the performance of mNGS in the diagnosis of TBM, and illustrate the sensitivity and specificity of different methods.Methods. We retrospectively recruited TBM patients between January 2021 and March 2023 to evaluate the performance of mNGS on cerebrospinal fluid (CSF) samples, in comparison with conventional microbiological testing, including culturing of Mycobacterium tuberculosis (MTB), acid-fast bacillus (AFB) stain, reverse transcription PCR and Xpert MTB/RIF.Results. Of the 40 enrolled, 34 participants were diagnosed with TBM, including 15(44.12 %) definite and 19(55.88 %) clinical diagnosis based upon clinical manifestations, CSF parameters, brain imaging, pathogen evidence and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MTBC) in 11 CSF samples. In patients with definite TBM, the sensitivity, specificity, positive predictive value, negative predictive value and accuracy of mNGS were 78.57, 100, 100, 66.67 and 85 %, respectively. Compared to conventional diagnostic methods, the sensitivity of mNGS (78.57 %) was higher than AFB (0 %), culturing (0 %), RT-PCR (60 %) and Xpert MTB/RIF (14.29 %).Conclusions. Our study indicates that mNGS of CSF exhibited an overall improved sensitivity over conventional diagnostic methods for TBM and can be considered a front-line CSF test.
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Affiliation(s)
- Bi-Wei Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, PR China
| | - Jian-Chen Hong
- Department of Gastrointestinal Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, PR China
| | - Zai-Jie Jiang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, PR China
| | - Wei-Qing Zhang
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, PR China
| | - Qi-Chao Fan
- Department of Infectious Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, PR China
| | - Xiang-Ping Yao
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, PR China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, PR China
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6
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Zayakin P. sRNAflow: A Tool for the Analysis of Small RNA-Seq Data. Noncoding RNA 2024; 10:6. [PMID: 38250806 PMCID: PMC10801628 DOI: 10.3390/ncrna10010006] [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: 11/21/2023] [Revised: 12/29/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
The analysis of small RNA sequencing data across a range of biofluids is a significant research area, given the diversity of RNA types that hold potential diagnostic, prognostic, and predictive value. The intricate task of segregating the complex mixture of small RNAs from both human and other species, including bacteria, fungi, and viruses, poses one of the most formidable challenges in the analysis of small RNA sequencing data, currently lacking satisfactory solutions. This study introduces sRNAflow, a user-friendly bioinformatic tool with a web interface designed for the analysis of small RNAs obtained from biological fluids. Tailored to the unique requirements of such samples, the proposed pipeline addresses various challenges, including filtering potential RNAs from reagents and environment, classifying small RNA types, managing small RNA annotation overlap, conducting differential expression assays, analysing isomiRs, and presenting an approach to identify the sources of small RNAs within samples. sRNAflow also encompasses an alternative alignment-free analysis of RNA-seq data, featuring clustering and initial RNA source identification using BLAST. This comprehensive approach facilitates meaningful comparisons of results between different analytical methods.
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Affiliation(s)
- Pawel Zayakin
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia;
- European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
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7
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Boruah AP, Kroopnick A, Thakkar R, Wapniarski AE, Kim C, Dugue R, Harrigan E, Lipkin WI, Mishra N, Thakur KT. Application of VirCapSeq-VERT and BacCapSeq in the diagnosis of presumed and definitive neuroinfectious diseases. J Neurovirol 2023; 29:678-691. [PMID: 37851324 DOI: 10.1007/s13365-023-01172-w] [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: 03/09/2023] [Revised: 03/09/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing sequencing costs and the complexity of bioinformatic analysis. Here we report the use of virus capture-based sequencing for vertebrate viruses (VirCapSeq-VERT) and bacterial capture sequencing (BacCapSeq) in investigating CNS infections. Thirty-four samples were categorized: (1) patients with definitive CNS infection by routine testing; (2) patients meeting clinically the Brighton criteria (BC) for meningoencephalitis; (3) patients with presumptive infectious etiology highest on the differential. RNA extracts from cerebrospinal fluid (CSF) were used for VirCapSeq-VERT, and DNA extracts were used for BacCapSeq analysis. Among 8 samples from known CNS infections in group 1, VirCapSeq and BacCapSeq confirmed 3 expected diagnoses (42.8%), were negative in 2 (25%), yielded an alternative result in 1 (11.1%), and did not detect 2 expected negative pathogens. The confirmed cases identified HHV-6, HSV-2, and VZV while the negative samples included JCV and HSV-2. In groups 2 and 3, 11/26 samples (42%) were positive for at least one pathogen; however, 27% of the total samples (7/26) were positive for commensal organisms. No microbial nucleic acids were detected in negative control samples. HTS showed limited promise for pathogen identification in presumed CNS infectious diseases in our small sample. Before conducting larger-scale prospective studies to assess the clinical value of this novel technique, clinicians should understand the benefits and limitations of using this modality.
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Affiliation(s)
- Abhilasha P Boruah
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
- Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Adam Kroopnick
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Anne E Wapniarski
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - Carla Kim
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - Rachelle Dugue
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - Eileen Harrigan
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Kiran T Thakur
- Department of Neurology, Columbia University Irving Medical Center/New York Presbyterian Hospital (CUIMC/NYP), New York, NY, USA.
- Division of Critical Care and Hospitalist Neurology, Department of Neurology, Milstein Hospital, 177 Fort Washington Avenue, New York, NY, 8GS-39910032, USA.
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Lee HJ, Lee Y, Hong SH, Park JW. Decoding the Link between Periodontitis and Neuroinflammation: The Journey of Bacterial Extracellular Vesicles. Curr Genomics 2023; 24:132-135. [PMID: 38178987 PMCID: PMC10761334 DOI: 10.2174/0113892029258657231010065320] [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: 04/19/2023] [Revised: 07/26/2023] [Accepted: 09/08/2023] [Indexed: 01/06/2024] Open
Affiliation(s)
- Heon-Jin Lee
- Department of Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea, South
| | - Youngkyun Lee
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea, South
| | - Su-Hyung Hong
- Department of Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea, South
| | - Jin-Woo Park
- Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea, South
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9
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Shin D, Kim J, Lee JH, Kim JI, Oh YM. Profiling of Microbial Landscape in Lung of Chronic Obstructive Pulmonary Disease Patients Using RNA Sequencing. Int J Chron Obstruct Pulmon Dis 2023; 18:2531-2542. [PMID: 38022823 PMCID: PMC10644840 DOI: 10.2147/copd.s426260] [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: 08/08/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose The aim of the study was to use RNA sequencing (RNA-seq) data of lung from chronic obstructive pulmonary disease (COPD) patients to identify the bacteria that are most commonly detected. Additionally, the study sought to investigate the differences in these infections between normal lung tissues and those affected by COPD. Patients and Methods We re-analyzed RNA-seq data of lung from 99 COPD patients and 93 non-COPD smokers to determine the extent to which the metagenomes differed between the two groups and to assess the reliability of the metagenomes. We used unmapped reads in the RNA-seq data that were not aligned to the human reference genome to identify more common infections in COPD patients. Results We identified 18 bacteria that exhibited significant differences between the COPD and non-COPD smoker groups. Among these, Yersinia enterocolitica was found to be more than 30% more abundant in COPD. Additionally, we observed difference in detection rate based on smoking history. To ensure the accuracy of our findings and distinguish them from false positives, we double-check the metagenomic profile using Basic Local Alignment Search Tool (BLAST). We were able to identify and remove specific species that might have been misclassified as other species in Kraken2 but were actually Staphylococcus aureus, as identified by BLAST analysis. Conclusion This study highlighted the method of using unmapped reads, which were not typically used in sequencing data, to identify microorganisms present in patients with lung diseases such as COPD. This method expanded our understanding of the microbial landscape in COPD and provided insights into the potential role of microorganisms in disease development and progression.
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Affiliation(s)
- Dongjin Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Juhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jang Ho Lee
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Genomic Medicine Institute, Seoul National University, Seoul, Republic of Korea
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Yeon-Mok Oh
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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10
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Boruah AP, Kroopnick A, Thakkar R, Wapniarski AE, Kim C, Dugue R, Harrigan E, Lipkin WI, Mishra N, Thakur KT. Application of VirCapSeq-VERT and BacCapSeq In the Diagnosis of Presumed and Definitive Neuroinfectious Diseases. RESEARCH SQUARE 2023:rs.3.rs-2675665. [PMID: 37502953 PMCID: PMC10371130 DOI: 10.21203/rs.3.rs-2675665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing sequencing costs and complexity of bioinformatic analysis. Here we report the use of virus capture based sequencing for vertebrate viruses (VirCapSeq-VERT) and bacterial capture sequencing (BacCapSeq) in investigating CNS infections. Design/Methods Thirty-four samples were categorized: (1) Patients with definitive CNS infection by routine testing; (2) Patients meeting clinically Brighton Criteria (BC) for meningoencephalitis (3) Patients with presumptive infectious etiology highest on the differential. RNA extracts from cerebrospinal fluid (CSF) were used for VirCapSeq-VERT and DNA extracts were used for BacCapSeq analysis. Results Among 8 samples from known CNS infections in group 1, VirCapSeq and BacCapSeq confirmed 3 expected diagnoses (42.8%), were negative in 2 (25%), yielded an alternative result in 1 (11.1%), and did not detect 2 expected negative pathogens. The confirmed cases identified HHV-6, HSV-2, and VZV while the negative samples included JCV and HSV-2. In groups 2 and 3,11/26 samples (42%) were positive for at least one pathogen, however 27% of the total samples (7/26) were positive for commensal organisms. No microbial nucleic acids were detected in negative control samples. Conclusions HTS showed limited promise for pathogen identification in presumed CNS infectious diseases in our small sample. Before conducting larger-scale prospective studies to assess clinical value of this novel technique, clinicians should understand benefits and limitations of using this modality.
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Affiliation(s)
| | | | | | | | | | | | | | - W Ian Lipkin
- Columbia University Mailman School of Public Health
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11
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Che Lah EF, Ahamad M, Dmitry A, Md Zain BM, Yaakop S. Metagenomic profile of the bacterial communities associated with Ixodes granulatus (Acari: Ixodidae): a potential vector of tick-borne diseases. JOURNAL OF MEDICAL ENTOMOLOGY 2023:7131392. [PMID: 37075471 DOI: 10.1093/jme/tjad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
Ixodes granulatus Supino, 1897 (Acari: Ixodida) is one of Malaysia's most common hard ticks and is a potential vector for tick-borne diseases (TBDs). Despite its great public health importance, research on I. granulatus microbial communities remains largely unexplored. Therefore, this study aimed to investigate the bacterial communities of on-host I. granulatus collected from three different recreational areas on the East Coast of Peninsular Malaysia using high throughput Next Generation Sequencing (NGS). A total of 9 females on-host I. granulatus were subjected to metabarcoding analysis targeting V3-V4 regions of 16S ribosomal RNA (rRNA) using the Illumina MiSeq platform. This study identified 15 bacterial phyla corresponding to 19 classes, 54 orders, and 90 families from 435 amplicon sequence variants (ASVs), revealing a diverse bacterial community profile. Together with 130 genera assigned, local I. granulatus harbored 4 genera of pathogens, i.e., Rickettsia da Rocha Lima, 1916 (Rickettsiales: Rickettsiaceae) (58.6%), Borrelia Swellengrebel 1907 (Spirochaetales: Borreliaceae) (31.6%), Borreliella Adeolu and Gupta 2015 (Spirochaetales: Borreliaceae) (0.6%), and Ehrlichia Cowdria Moshkovski 1947 (Rickettsiales: Ehrlichiaceae) (39.9%). Some endosymbiont bacteria, such as Coxiella (Philip, 1943) (Legionellales: Coxiellaceae), Wolbachia Hertig 1936 (Rickettsiales: Ehrlichiaceae), and Rickettsiella Philip, 1956 (Legionellales: Coxiellaceae), were also detected at very low abundance. Interestingly, this study reported the co-infection of Borrelia and Ehrlichia for the first time, instilling potential health concerns in the context of co-transmission to humans, especially in areas with a high population of I. granulatus. This study successfully characterized the tick microbiome and provided the first baseline data of I. granulatus bacterial communities in Malaysia. These results support the need for way-forward research on tick-associated bacteria using NGS, focusing on medically important species toward TBD prevention.
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Affiliation(s)
- Ernieenor Faraliana Che Lah
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research (IMR), National Institutes of Health, Ministry of Health Malaysia, Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, Shah Alam, Selangor 40170, Malaysia
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia
| | - Mariana Ahamad
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research (IMR), National Institutes of Health, Ministry of Health Malaysia, Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, Shah Alam, Selangor 40170, Malaysia
| | - Apanaskevich Dmitry
- United States National Tick Collection, The James H. Oliver, Jr. Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA 30460-8042, USA
| | - Badrul Munir Md Zain
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia
| | - Salmah Yaakop
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia
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12
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Liu Y, Elworth RAL, Jochum MD, Aagaard KM, Treangen TJ. De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee. Nat Commun 2022; 13:6799. [PMID: 36357382 PMCID: PMC9649624 DOI: 10.1038/s41467-022-34409-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 10/25/2022] [Indexed: 11/12/2022] Open
Abstract
Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low-biomass environments. Contamination from DNA extraction kits or sampling lab environments leaves taxonomic "bread crumbs" across multiple distinct sample types. Here we describe Squeegee, a de novo contamination detection tool that is based upon this principle, allowing the detection of microbial contaminants when negative controls are unavailable. On the low-biomass samples, we compare Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers putative contaminants. We analyze samples of varying biomass from the Human Microbiome Project and identify likely, previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision and thus represents a computational approach for contaminant detection when negative controls are unavailable.
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Affiliation(s)
- Yunxi Liu
- Rice University, Department of Computer Science, Houston, TX, 77005, USA
| | - R A Leo Elworth
- Rice University, Department of Computer Science, Houston, TX, 77005, USA
| | - Michael D Jochum
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
| | - Kjersti M Aagaard
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
| | - Todd J Treangen
- Rice University, Department of Computer Science, Houston, TX, 77005, USA.
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13
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Ferreira-Neto JRC, de Araújo FC, de Oliveira Silva RL, de Melo NF, Pandolfi V, Frosi G, de Lima Morais DA, da Silva MD, Rivas R, Santos MG, de Tarso Aidar S, Morgante CV, Benko-Iseppon AM. Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations. PHYSIOLOGIA PLANTARUM 2022; 174:e13821. [PMID: 36345266 DOI: 10.1111/ppl.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Stylosanthes scabra, popularly known as stylo, is native to the Brazilian Caatinga semiarid region and stands out as a drought-tolerant shrub forage crop. This work provides information about the plant response during the first 48 h of water deficit, followed by a rehydration treatment. Besides root transcriptomics data, 13 physiological or biochemical parameters were scrutinized. Additionally, RNA-Seq annotated transcripts not associated with the "Viridiplantae" clade were taxonomically categorized. It was found that S. scabra quickly perceives and recovers from the oscillations of the imposed water regime. Physiologically, mechanisms that minimize evapotranspiration or protect the photosynthetic apparatus stood out. Biochemically, it was found that the root tissue invests in synthesizing compounds that can act as osmolytes (proline and sugars), emphasizing the importance of osmoregulation to water deficit acclimation. Consistently, transcriptome and qPCR analyses showed that a set of enriched biological processes with upregulated (UR) transcripts were involved in protective functions against reactive oxygen species or encoding enzymes of important metabolic pathways, which might contribute to S. scabra response to water deficit. Additionally, several UR kinases and transcription factors were identified. Finally, in an innovative approach, some naturally occurring microbial groups (such as Schizosaccharomyces, Bradyrhizobium, etc.) were identified in the S. scabra roots. This study reveals insights into the physiological, biochemical, and molecular mechanisms underlying the S. scabra response to water deficit and provides candidate genes that may be useful in developing drought-tolerant crop varieties through biotechnological applications.
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Affiliation(s)
- José Ribamar Costa Ferreira-Neto
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Flávia Czekalski de Araújo
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Roberta Lane de Oliveira Silva
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | | | - Valesca Pandolfi
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Gabriella Frosi
- Départament de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Manassés Daniel da Silva
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Rebeca Rivas
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Mauro Guida Santos
- Laboratório de Fisiologia Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Saulo de Tarso Aidar
- Empresa Brasileira de Pesquisa Agropecuária (SEMIÁRIDO), Petrolina, Pernambuco, Brazil
| | | | - Ana Maria Benko-Iseppon
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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14
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Chen Y, Fan L, Chai Y, Xu J. Advantages and challenges of metagenomic sequencing for the diagnosis of pulmonary infectious diseases. THE CLINICAL RESPIRATORY JOURNAL 2022; 16:646-656. [PMID: 36068680 PMCID: PMC9527156 DOI: 10.1111/crj.13538] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/18/2022] [Accepted: 08/15/2022] [Indexed: 11/28/2022]
Abstract
Objective We aim to familiarize the application status of metagenomic sequencing in diagnosing pulmonary infections, to compare metagenomic sequencing with traditional diagnostic methods, to conclude the advantages and limitations of metagenomic sequencing, and to provide some advice for clinical practice and some inspiration for associated researches. Data Sources The data were obtained from peer‐reviewed literature, white papers, and meeting reports. Results This review focused on the applications of untargeted metagenomic sequencing in lungs infected by bacteria, viruses, fungi, chlamydia pneumoniae, Mycoplasma pneumoniae, parasites, and other pathogens. Compared with conventional diagnostic methods, metagenomic sequencing is better in detecting novel, rare, and unexpected pathogens and being applied in co‐infections. Meanwhile, it can also provide more comprehensive information about pathogens. However, metagenomic sequencing still has limitations. Also, the situations that should be applied in and how the results should be interpreted are discussed in this review. Conclusion Metagenomic sequencing improves efficiency to identify pathogens compared with traditional diagnostic methods and can be applied in clinical diagnosis. However, the technology of metagenomic sequencing still needs to be improved. Also, clinicians should learn more about when to use metagenomic sequencing and how to interpret its results.
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Affiliation(s)
- Yan Chen
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Institute of Respiratory Medicine Tongji University School of Medicine Shanghai China
| | - Li‐Chao Fan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Institute of Respiratory Medicine Tongji University School of Medicine Shanghai China
| | - Yan‐Hua Chai
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Institute of Respiratory Medicine Tongji University School of Medicine Shanghai China
| | - Jin‐Fu Xu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Institute of Respiratory Medicine Tongji University School of Medicine Shanghai China
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15
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CleanSeq: A Pipeline for Contamination Detection, Cleanup, and Mutation Verifications from Microbial Genome Sequencing Data. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12126209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Contaminations frequently occur in bacterial cultures, which significantly affect the reproducibility and reliability of the results from whole-genome sequencing (WGS). Decontaminated WGS data with clean reads is the only desirable source for detecting possible variants correctly. Improvements in bioinformatics are essential to analyze the contaminated WGS dataset. Existing pipelines usually contain contamination detection, decontamination, and variant calling separately. The efficiency and results from existing pipelines fluctuate since distinctive computational models and parameters are applied. It is then promising to develop a bioinformatical tool containing functions to discriminate and remove contaminated reads and improve variant calling from clean reads. In this study, we established a Python-based pipeline named CleanSeq for automatic detection and removal of contaminating reads, analyzing possible genome variants with proper verifications via local re-alignments. The application and reproducibility are proven in either simulated, publicly available datasets or actual genome sequencing reads from our experimental evolution study in Escherichia coli. We successfully obtained decontaminated reads, called out all seven consistent mutations from the contaminated bacterial sample, and derived five colonies. Collectively, the results demonstrated that CleanSeq could effectively process the contaminated samples to achieve decontaminated reads, based on which reliable results (i.e., variant calling) could be obtained.
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16
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The human "contaminome": bacterial, viral, and computational contamination in whole genome sequences from 1000 families. Sci Rep 2022; 12:9863. [PMID: 35701436 PMCID: PMC9198055 DOI: 10.1038/s41598-022-13269-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/18/2022] [Indexed: 01/11/2023] Open
Abstract
The unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1000 families and nearly 5000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies. We present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes. Both experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.
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17
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Ko KKK, Chng KR, Nagarajan N. Metagenomics-enabled microbial surveillance. Nat Microbiol 2022; 7:486-496. [PMID: 35365786 DOI: 10.1038/s41564-022-01089-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
Lessons learnt from the COVID-19 pandemic include increased awareness of the potential for zoonoses and emerging infectious diseases that can adversely affect human health. Although emergent viruses are currently in the spotlight, we must not forget the ongoing toll of morbidity and mortality owing to antimicrobial resistance in bacterial pathogens and to vector-borne, foodborne and waterborne diseases. Population growth, planetary change, international travel and medical tourism all contribute to the increasing frequency of infectious disease outbreaks. Surveillance is therefore of crucial importance, but the diversity of microbial pathogens, coupled with resource-intensive methods, compromises our ability to scale-up such efforts. Innovative technologies that are both easy to use and able to simultaneously identify diverse microorganisms (viral, bacterial or fungal) with precision are necessary to enable informed public health decisions. Metagenomics-enabled surveillance methods offer the opportunity to improve detection of both known and yet-to-emerge pathogens.
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Affiliation(s)
- Karrie K K Ko
- Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore, Singapore.,Department of Microbiology, Singapore General Hospital, Singapore, Singapore.,Department of Molecular Pathology, Singapore General Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National Univerisity of Singapore, Singapore, Singapore
| | - Kern Rei Chng
- Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore, Singapore.,National Centre for Food Science, Singapore Food Agency, Singapore, Singapore
| | - Niranjan Nagarajan
- Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore, Singapore. .,Yong Loo Lin School of Medicine, National Univerisity of Singapore, Singapore, Singapore.
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18
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Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics. Sci Rep 2022; 12:3378. [PMID: 35233021 PMCID: PMC8888594 DOI: 10.1038/s41598-022-07260-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 02/04/2022] [Indexed: 12/25/2022] Open
Abstract
Infection in the central nervous system is a severe condition associated with high morbidity and mortality. Despite ample testing, the majority of encephalitis and meningitis cases remain undiagnosed. Metagenomic sequencing of cerebrospinal fluid has emerged as an unbiased approach to identify rare microbes and novel pathogens. However, several major hurdles remain, including establishment of individual limits of detection, removal of false positives and implementation of universal controls. Twenty-one cerebrospinal fluid samples, in which a known pathogen had been positively identified by available clinical techniques, were subjected to metagenomic DNA sequencing. Fourteen samples contained minute levels of Epstein-Barr virus. The detection threshold for each sample was calculated by using the total leukocyte content in the sample and environmental contaminants found in the bioinformatic classifiers. Virus sequences were detected in all ten samples, in which more than one read was expected according to the calculations. Conversely, no viral reads were detected in seven out of eight samples, in which less than one read was expected according to the calculations. False positive pathogens of computational or environmental origin were readily identified, by using a commonly available cell control. For bacteria, additional filters including a comparison between classifiers removed the remaining false positives and alleviated pathogen identification. Here we show a generalizable method for identification of pathogen species using DNA metagenomic sequencing. The choice of bioinformatic method mainly affected the efficiency of pathogen identification, but not the sensitivity of detection. Identification of pathogens requires multiple filtering steps including read distribution, sequence diversity and complementary verification of pathogen reads.
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19
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Shi Y, Wang G, Lau HCH, Yu J. Metagenomic Sequencing for Microbial DNA in Human Samples: Emerging Technological Advances. Int J Mol Sci 2022; 23:ijms23042181. [PMID: 35216302 PMCID: PMC8877284 DOI: 10.3390/ijms23042181] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Whole genome metagenomic sequencing is a powerful platform enabling the simultaneous identification of all genes from entirely different kingdoms of organisms in a complex sample. This technology has revolutionised multiple areas from microbiome research to clinical diagnoses. However, one of the major challenges of a metagenomic study is the overwhelming non-microbial DNA present in most of the host-derived specimens, which can inundate the microbial signals and reduce the sensitivity of microorganism detection. Various host DNA depletion methods to facilitate metagenomic sequencing have been developed and have received considerable attention in this context. In this review, we present an overview of current host DNA depletion approaches along with explanations of their underlying principles, advantages and disadvantages. We also discuss their applications in laboratory microbiome research and clinical diagnoses and, finally, we envisage the direction of the further perfection of metagenomic sequencing in samples with overabundant host DNA.
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Affiliation(s)
| | | | | | - Jun Yu
- Correspondence: ; Tel.: +852-37636099; Fax:+852-21445330
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20
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Corredor Z, Suarez-Molina A, Fong C, Cifuentes-C L, Guauque-Olarte S. Presence of periodontal pathogenic bacteria in blood of patients with coronary artery disease. Sci Rep 2022; 12:1241. [PMID: 35075206 PMCID: PMC8786953 DOI: 10.1038/s41598-022-05337-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
It has been hypothesised that oral bacteria can migrate, through the blood, from the mouth to the arterial plaques, thus exacerbating atherosclerosis. This study compared bacteria present in the peripheral blood of individuals with and without coronary artery disease (CAD). RNA sequences obtained from blood were downloaded from GEO (GSE58150). Eight patients with coronary artery calcification (CAC) scoring > 500 and eight healthy individuals were analysed. After conducting quality control, the sequences were aligned to the hg38 reference genome using Hisat2. Bacterial taxa were analysed by inputting the unmapped sequences into Kraken. Ecological indices were calculated using Vegan. The package DESeq2 was used to compare the counts of bacteria per standard rank between groups. A total of 51 species were found only in patients with CAD and 41 were exclusively present in healthy individuals. The counts of one phylum, one class, three orders, two families and one genus were significantly different between the analysed groups (p < 0.00032, FDR < 10%), including the orders Cardiobacteriales, Corynebacteriales and Fusobacteriales. Twenty-three bacterial species belonging to the subgingival plaque bacterial complexes were also identified in the blood of individuals from both the groups; Fusobacterium nucleatum was significantly less frequent in patients with CAD (p = 0.0012, FDR = 4.8%). Furthermore, the frequency of another 11 bacteria differed significantly among patients with CAD than that among healthy individuals (p < 0.0030, FDR < 10%). These bacteria have not been previously reported in patients with atherosclerosis and periodontitis. The presence of members of the subgingival plaque bacterial complexes in the blood of patients with CAC supports the hypothesis that the periodontopathogens can be disseminated through the blood flow to other body parts where they may enhance inflammatory processes that can lead to the development or exacerbation of atherosclerosis.
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Affiliation(s)
- Zuray Corredor
- Faculty of Dentistry, Universidad Cooperativa de Colombia Campus Pasto, Pasto, Colombia
| | | | - Cristian Fong
- Faculty of Medicine, Universidad Cooperativa de Colombia Campus Santa Marta, Santa Marta, Colombia
| | - Laura Cifuentes-C
- Faculty of Dentistry, Universidad Cooperativa de Colombia Campus Pasto, Pasto, Colombia
| | - Sandra Guauque-Olarte
- GIOM Group, Faculty of Dentistry, Universidad Cooperativa de Colombia Campus Envigado, Cra. 47 No. 37 sur 18, Envigado, Antioquia, Colombia.
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21
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Mortezaei Z. Computational methods for analyzing RNA-sequencing contaminated samples and its impact on cancer genome studies. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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22
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Assessing the Iatrogenic Contribution to Contamination During Root Canal Treatment. J Endod 2022; 48:479-486. [DOI: 10.1016/j.joen.2022.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/22/2021] [Accepted: 01/13/2022] [Indexed: 12/14/2022]
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23
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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: 20] [Impact Index Per Article: 6.7] [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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24
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Bu Y, Chan YK, Wong HL, Poon SHL, Lo ACY, Shih KC, Tong L. A Review of the Impact of Alterations in Gut Microbiome on the Immunopathogenesis of Ocular Diseases. J Clin Med 2021; 10:jcm10204694. [PMID: 34682816 PMCID: PMC8541376 DOI: 10.3390/jcm10204694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/01/2021] [Accepted: 10/09/2021] [Indexed: 12/11/2022] Open
Abstract
Recent studies have highlighted the association between ocular diseases and microbiota profiles of the host intestinal tract and oral cavity. There is mounting evidence supporting the existence of a 'gut-eye axis', whereby changes in gut microbiome alter host immunity, with consequential implications for ocular health and disease. In this review, we examined recent published findings on the association between gut microbiome and ocular morbidity, based on 25 original articles published between 2011 to 2020. The review included both clinical and in vivo animal studies, with particular focus on the influence of the microbiome on host immunity and metabolism. Significant associations between altered intestinal microbiome and specific ocular diseases and pathological processes, including Behçet's syndrome, autoimmune uveitis, age-related macular degeneration, choroidal neovascularization, bacterial keratitis, and Sjögren-like lacrimal keratoconjunctivitis have been demonstrated. Furthermore, alterations in the gut microbiome resulted in quantifiable changes in the host immune response, suggesting immunopathogenesis as the basis for the link between intestinal dysbiosis and ocular disease. We also examined and compared different techniques used in the identification and quantification of gut microorganisms. With our enhanced understanding of the potential role of gut commensals in ophthalmic disease, the stage is set for further studies on the underlying mechanisms linking the gut microbiome, the host immune response, and the pathogenesis of ophthalmic disease.
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Affiliation(s)
- Yashan Bu
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Yau-Kei Chan
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Ho-Lam Wong
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Stephanie Hiu-Ling Poon
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Amy Cheuk-Yin Lo
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Kendrick Co Shih
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
- Correspondence:
| | - Louis Tong
- Cornea and External Eye Disease Service, Singapore National Eye Centre, Singapore 168751, Singapore;
- Ocular Surface Research Group, Singapore Eye Research Institute, Singapore 169856, Singapore
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Evaluation of a high-throughput, cost-effective Illumina library preparation kit. Sci Rep 2021; 11:15925. [PMID: 34354114 PMCID: PMC8342411 DOI: 10.1038/s41598-021-94911-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
Library preparation for high-throughput sequencing applications is a critical step in producing representative, unbiased sequencing data. The iGenomX Riptide High Throughput Rapid Library Prep Kit purports to provide high-quality sequencing data with lower costs compared to other Illumina library kits. To test these claims, we compared sequence data quality of Riptide libraries to libraries constructed with KAPA Hyper and NEBNext Ultra. Across several single-source genome samples, mapping performance and de novo assembly of Riptide libraries were similar to conventional libraries prepared with the same DNA. Poor performance of some libraries resulted in low sequencing depth. In particular, degraded DNA samples may be challenging to sequence with Riptide. There was little cross-well plate contamination with the overwhelming majority of reads belong to the proper source genomes. The sequencing of metagenome samples using different Riptide primer sets resulted in variable taxonomic assignment of reads. Increased adoption of the Riptide kit will decrease library preparation costs. However, this method might not be suitable for degraded DNA.
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26
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Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M, Ashford B. Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Brief Bioinform 2021; 22:6330938. [PMID: 34329375 DOI: 10.1093/bib/bbab259] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
Significant innovations in next-generation sequencing techniques and bioinformatics tools have impacted our appreciation and understanding of RNA. Practical RNA sequencing (RNA-Seq) applications have evolved in conjunction with sequence technology and bioinformatic tools advances. In most projects, bulk RNA-Seq data is used to measure gene expression patterns, isoform expression, alternative splicing and single-nucleotide polymorphisms. However, RNA-Seq holds far more hidden biological information including details of copy number alteration, microbial contamination, transposable elements, cell type (deconvolution) and the presence of neoantigens. Recent novel and advanced bioinformatic algorithms developed the capacity to retrieve this information from bulk RNA-Seq data, thus broadening its scope. The focus of this review is to comprehend the emerging bulk RNA-Seq-based analyses, emphasizing less familiar and underused applications. In doing so, we highlight the power of bulk RNA-Seq in providing biological insights.
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Affiliation(s)
- Amarinder Singh Thind
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Isha Monga
- Columbia University, New York City, NY, USA
| | | | - Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | | | - Marie Ranson
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Bruce Ashford
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
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27
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Cordoba J, Perez E, Van Vlierberghe M, Bertrand AR, Lupo V, Cardol P, Baurain D. De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis. Genes (Basel) 2021; 12:842. [PMID: 34072576 PMCID: PMC8227486 DOI: 10.3390/genes12060842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023] Open
Abstract
Euglena gracilis is a well-known photosynthetic microeukaryote considered as the product of a secondary endosymbiosis between a green alga and a phagotrophic unicellular belonging to the same eukaryotic phylum as the parasitic trypanosomatids. As its nuclear genome has proven difficult to sequence, reliable transcriptomes are important for functional studies. In this work, we assembled a new consensus transcriptome by combining sequencing reads from five independent studies. Based on a detailed comparison with two previously released transcriptomes, our consensus transcriptome appears to be the most complete so far. Remapping the reads on it allowed us to compare the expression of the transcripts across multiple culture conditions at once and to infer a functionally annotated network of co-expressed genes. Although the emergence of meaningful gene clusters indicates that some biological signal lies in gene expression levels, our analyses confirm that gene regulation in euglenozoans is not primarily controlled at the transcriptional level. Regarding the origin of E. gracilis, we observe a heavily mixed gene ancestry, as previously reported, and rule out sequence contamination as a possible explanation for these observations. Instead, they indicate that this complex alga has evolved through a convoluted process involving much more than two partners.
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Affiliation(s)
- Javier Cordoba
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Emilie Perez
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Mick Van Vlierberghe
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Amandine R. Bertrand
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Valérian Lupo
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Pierre Cardol
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Denis Baurain
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
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28
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Lopes ALK, Kriegová E, Lukeš J, Krieger MA, Ludwig A. Distribution of Merlin in eukaryotes and first report of DNA transposons in kinetoplastid protists. PLoS One 2021; 16:e0251133. [PMID: 33956864 PMCID: PMC8101967 DOI: 10.1371/journal.pone.0251133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 04/21/2021] [Indexed: 11/19/2022] Open
Abstract
DNA transposons are defined as repeated DNA sequences that can move within the host genome through the action of transposases. The transposon superfamily Merlin was originally found mainly in animal genomes. Here, we describe a global distribution of the Merlin in animals, fungi, plants and protists, reporting for the first time their presence in Rhodophyceae, Metamonada, Discoba and Alveolata. We identified a great variety of potentially active Merlin families, some containing highly imperfect terminal inverted repeats and internal tandem repeats. Merlin-related sequences with no evidence of mobilization capacity were also observed and may be products of domestication. The evolutionary trees support that Merlin is likely an ancient superfamily, with early events of diversification and secondary losses, although repeated re-invasions probably occurred in some groups, which would explain its diversity and discontinuous distribution. We cannot rule out the possibility that the Merlin superfamily is the product of multiple horizontal transfers of related prokaryotic insertion sequences. Moreover, this is the first account of a DNA transposon in kinetoplastid flagellates, with conserved Merlin transposase identified in Bodo saltans and Perkinsela sp., whereas it is absent in trypanosomatids. Based on the level of conservation of the transposase and overlaps of putative open reading frames with Merlin, we propose that in protists it may serve as a raw material for gene emergence.
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Affiliation(s)
- Ana Luisa Kalb Lopes
- Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, PR, Brazil
- Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brazil
| | - Eva Kriegová
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Marco Aurélio Krieger
- Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, PR, Brazil
| | - Adriana Ludwig
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, PR, Brazil
- * E-mail:
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29
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Comprehensive comparative genomics reveals over 50 phyla of free-living and pathogenic bacteria are associated with diverse members of the amoebozoa. Sci Rep 2021; 11:8043. [PMID: 33850182 PMCID: PMC8044228 DOI: 10.1038/s41598-021-87192-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
The Amoebozoa, a group containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics/transcriptomics to investigate the association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (64) and human pathogen genera (51) associated with the Amoebozoa. Using single cell genomics/transcriptomics we were able to determine up to 24 potential endosymbiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multi-drug resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern.
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30
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Anifandis G, Tempest HG, Oliva R, Swanson GM, Simopoulou M, Easley CA, Primig M, Messini CI, Turek PJ, Sutovsky P, Ory SJ, Krawetz SA. COVID-19 and human reproduction: A pandemic that packs a serious punch. Syst Biol Reprod Med 2021; 67:3-23. [PMID: 33719829 DOI: 10.1080/19396368.2020.1855271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic has led to a worldwide health emergency that has impacted 188 countries at last count. The rapid community transmission and relatively high mortality rates with COVID-19 in modern times are relatively unique features of this flu pandemic and have resulted in an unparalleled global health crisis. SARS-CoV-2, being a respiratory virus, mainly affects the lungs, but is capable of infecting other vital organs, such as brain, heart and kidney. Emerging evidence suggests that the virus also targets male and female reproductive organs that express its main receptor ACE2, although it is as yet unclear if this has any implications for human fertility. Furthermore, professional bodies have recommended discontinuing fertility services during the pandemic such that reproductive services have also been affected. Although increased safety measures have helped to mitigate the propagation of COVID-19 in a number of countries, it seems that there is no predictable timeline to containment of the virus, a goal likely to remain elusive until an effective vaccine becomes available and widely distributed across the globe. In parallel, research on reproduction has been postponed for obvious reasons, while diagnostic tests that detect the virus or antibodies against it are of vital importance to support public health policies, such as social distancing and our obligation to wear masks in public spaces. This review aims to provide an overview of critical research and ethics issues that have been continuously emerging in the field of reproductive medicine as the COVID-19 pandemic tragically unfolds.Abbreviations: ACE2: angiotensin- converting enzyme 2; ART: Assisted reproductive technology; ASRM: American Society for Reproductive Medicine; CCR9: C-C Motif Chemokine Receptor 9; CDC: Centers for Disease Control and Prevention; COVID-19: Coronavirus disease 2019; Ct: Cycle threshold; CXCR6: C-X-C Motif Chemokine Receptor 6; ELISA: enzyme-linked immunosorbent assay; ESHRE: European Society of Human Reproduction and Embryology; ET: Embryo transfer; FSH: Follicle Stimulating Hormone; FFPE: formalin fixed paraffin embedded; FYCO1: FYVE And Coiled-Coil Domain Autophagy Adaptor 1; IFFS: International Federation of Fertility Societies; IUI: Intrauterine insemination; IVF: In vitro fertilization; LH: Luteinizing Hormone; LZTFL1: Leucine Zipper Transcription Factor Like 1; MAR: medically assisted reproduction services; MERS: Middle East Respiratory syndrome; NGS: Next Generation Sequencing; ORF: Open Reading Frame; PPE: personal protective equipment; RE: RNA Element; REDa: RNA Element Discovery algorithm; RT-PCR: Reverse=trascriptase transcriptase-polymerase chain reaction; SARS: Severe acute respiratory syndrome; SARS-CoV-2: Severe Acute Respiratory Syndrome Coronavirus 2; SLC6A20: Solute Carrier Family 6 Member 20; SMS: Single Molecule Sequencing; T: Testosterone; TMPRSS2: transmembrane serine protease 2; WHO: World Health Organization; XCR1: X-C Motif Chemokine Receptor.
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Affiliation(s)
- George Anifandis
- Department of Obstetrics and Gynecology, School of Health Sciences, Faculty of Medicine, University of Thessaly, Larisa, Greece
| | - Helen G Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat De Barcelona, and Hospital Clinic from Barcelona, Spain
| | - Grace M Swanson
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Mara Simopoulou
- Department of Experimental Physiology, School of Health Sciences, Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece, Athens, Greece
| | - Charles A Easley
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.,Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Michael Primig
- Inserm, EHESP, Irset (Institut De Recherche En Santé, Environnement Et Travail), Rennes, France
| | - Christina I Messini
- Department of Obstetrics and Gynecology, School of Health Sciences, Faculty of Medicine, University of Thessaly, Larisa, Greece
| | - Paul J Turek
- It is a private Clinic, The Turek Clinic, Beverly Hills, CA, USA
| | - Peter Sutovsky
- Division of Animal Sciences and the Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO, USA
| | - Steve J Ory
- It is a private Clinic, IVF Florida Reproductive Institutes, Margate, FL, USA.,Department of Obstetrics and Gynecology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology and Center of Molecular Medicine and Genetics, C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI, USA
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31
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Fitzpatrick AH, Rupnik A, O'Shea H, Crispie F, Keaveney S, Cotter P. High Throughput Sequencing for the Detection and Characterization of RNA Viruses. Front Microbiol 2021; 12:621719. [PMID: 33692767 PMCID: PMC7938315 DOI: 10.3389/fmicb.2021.621719] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.
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Affiliation(s)
- Amy H. Fitzpatrick
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
- Shellfish Microbiology, Marine Institute, Oranmore, Ireland
- Biological Sciences, Munster Technological University, Cork, Ireland
| | | | - Helen O'Shea
- Biological Sciences, Munster Technological University, Cork, Ireland
| | - Fiona Crispie
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
| | | | - Paul Cotter
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
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32
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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33
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Chen X, Li D. Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data. Genomics 2021; 113:1189-1198. [PMID: 33301893 PMCID: PMC7856238 DOI: 10.1016/j.ygeno.2020.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/25/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
Numerous viral sequences have been reported in the whole-genome sequencing (WGS) data of human blood. However, it is not clear to what degree the virus-mappable reads represent true viral sequences rather than random-mapping or noise originating from sample preparation, sequencing processes, or other sources. Identification of patterns of virus-mappable reads may generate novel indicators for evaluating the origins of these viral sequences. We characterized paired-end unmapped reads and reads aligned to viral references in human WGS datasets, then compared patterns of the virus-mappable reads among DNA sources and sequencing facilities which produced these datasets. We then examined potential origins of the source- and facility-associated viral reads. The proportions of clean unmapped reads among the seven sequencing facilities were significantly different (P < 2 × 10-16). We identified 260,339 reads that were mappable to a total of 99 viral references in 2535 samples. The majority (86.7%) of these virus-mappable reads (corresponding to 47 viral references), which can be classified into four groups based on their distinct patterns, were strongly associated with sequencing facility or DNA source (adjusted P value <0.01). Possible origins of these reads include artificial sequences in library preparation, recombinant vectors in cell culture, and phages co-contaminated with their host bacteria. The sequencing facility-associated virus-mappable reads and patterns were repeatedly observed in other datasets produced in the same facilities. We have constructed an analytic framework and profiled the unmapped reads mappable to viral references. The results provide a new understanding of sequencing facility- and DNA source-associated batch effects in deep sequencing data and may facilitate improved bioinformatics filtering of reads.
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Affiliation(s)
- Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Department of Computer Science, University of Vermont, Burlington, VT 05405, USA; Neuroscience, Behavior, Health Initiative, University of Vermont, Burlington, VT 05405, USA.
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34
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Qian L, Shi Y, Li F, Wang Y, Ma M, Zhang Y, Shao YW, Zheng G, Zhang G. Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of External Ventricular and Lumbar Drainage-Associated Ventriculitis and Meningitis. Front Microbiol 2021; 11:596175. [PMID: 33381092 PMCID: PMC7767851 DOI: 10.3389/fmicb.2020.596175] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/13/2020] [Indexed: 12/20/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has become a widely used technology that can accurately detect individual pathogens. This prospective study was performed between February 2019 and September 2019 in one of the largest clinical neurosurgery centers in China. The study aimed to evaluate the performance of mNGS on cerebrospinal fluid (CSF) from neurosurgical patients for the diagnosis of external ventricular and lumbar drainage (EVD/LD)-associated ventriculitis and meningitis (VM). We collected CSF specimens from neurosurgical patients with EVD/LD for more than 24 h to perform conventional microbiological studies and mNGS analyses in a pairwise manner. We also investigated the usefulness of mNGS of CSF for the diagnosis of EVD/LD-associated VM. In total, 102 patients were enrolled in this study and divided into three groups, including confirmed VM (cVM) (39), suspected VM (sVM) (49), and non-VM (nVM) (14) groups. Of all the patients, mNGS detected 21 Gram-positive bacteria, 20 Gram-negative bacteria, and five fungi. The three primary bacteria detected were Staphylococcus epidermidis (9), Acinetobacter baumannii (5), and Staphylococcus aureus (3). The mNGS-positive coincidence rate of confirmed EVD/LD-associated VM was 61.54% (24/39), and the negative coincidence rate of the nVM group was 100% (14/14). Of 15 VM pathogens not identified by mNGS in the cVM group, eight were negative with mNGS and seven were inconsistent with the conventional microbiological identification results. In addition, mNGS identified pathogens in 22 cases that were negative using conventional methods; of them, 10 patients received a favorable clinical treatment; thus, showing the benefit of mNGS-guided therapy.
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Affiliation(s)
- Lingye Qian
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yijun Shi
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fangqiang Li
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yufei Wang
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Miao Ma
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanfang Zhang
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yang W Shao
- Nanjing Geneseeq Technology Inc., Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guanghui Zheng
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guojun Zhang
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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35
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Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas. Cell Rep 2020; 33:108552. [PMID: 33378673 DOI: 10.1016/j.celrep.2020.108552] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/14/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
Extracellular RNAs present in biofluids have emerged as potential biomarkers for disease. Where most studies focus on blood-derived fluids, other biofluids may be more informative. We present an atlas of messenger, circular, and small RNA transcriptomes of a comprehensive collection of 20 human biofluids. By means of synthetic spike-in controls, we compare RNA content across biofluids, revealing a 10,000-fold difference in concentration. The circular RNA fraction is increased in most biofluids compared to tissues. Each biofluid transcriptome is enriched for RNA molecules derived from specific tissues and cell types. Our atlas enables an informed selection of the most relevant biofluid to monitor particular diseases. To verify the biomarker potential in these biofluids, four validation cohorts representing a broad spectrum of diseases were profiled, revealing numerous differential RNAs between case and control subjects. Spike-normalized data are publicly available in the R2 web portal for further exploration.
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36
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Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR, Simner PJ. Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients. mBio 2020; 11:e01969-20. [PMID: 33219095 PMCID: PMC7686804 DOI: 10.1128/mbio.01969-20] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients (Shannon diversity index, P = 0.0082; Chao richness estimate, P = 0.0097; Simpson diversity index, P = 0.018), and differences in microbial communities were linked to disease severity (P = 0.022). Furthermore, statistically significant shifts in the microbiome were identified among SARS-CoV-2-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae (P = 0.028) and a reduction in the abundance of Corynebacterium accolens (P = 0.025) were observed. Our study corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages rather than the severity of COVID-19. Further, we demonstrate that SARS-CoV-2 causes a significant change in the respiratory microbiome. This work illustrates the utility of mNGS for the detection of SARS-CoV-2, for diagnosing coinfections without viral target enrichment or amplification, and for the analysis of the respiratory microbiome.IMPORTANCE SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to coinfections or the presence of other organisms that may impact SARS-CoV-2 disease progression and prognosis. Here, using direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing of NP swab specimens from 50 patients under investigation for COVID-19, we detected SARS-CoV-2 sequences by applying the CosmosID bioinformatics platform. Further, we characterized coinfections and detected a decrease in the diversity of the microbiomes in these patients. Statistically significant shifts in the microbiome were identified among COVID-19-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae and a reduction in the abundance of Corynebacterium accolens were observed. Our study also corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages of disease rather than with severity of disease. This work illustrates the utility of mNGS for the detection and analysis of SARS-CoV-2 from NP swabs without viral target enrichment or amplification and for the analysis of the respiratory microbiome.
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Affiliation(s)
- Heba H Mostafa
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John A Fissel
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Yehudit Bergman
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Victoria Gniazdowski
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Karen C Carroll
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rita R Colwell
- CosmosID, Inc., Rockville, Maryland, USA
- University of Maryland College Park, Institute for Advanced Computer Studies, College Park, Maryland, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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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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Sielemann K, Hafner A, Pucker B. The reuse of public datasets in the life sciences: potential risks and rewards. PeerJ 2020; 8:e9954. [PMID: 33024631 PMCID: PMC7518187 DOI: 10.7717/peerj.9954] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
The 'big data' revolution has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the associated challenges, limitations and risks. Possible solutions to issues and research integrity considerations are also discussed. Due to the prominence, abundance and wide distribution of sequencing data, we focus on the reuse of publicly available sequence datasets. We define 'successful reuse' as the use of previously published data to enable novel scientific findings. By using selected examples of successful reuse from different disciplines, we illustrate the enormous potential of the practice, while acknowledging the respective limitations and risks. A checklist to determine the reuse value and potential of a particular dataset is also provided. The open discussion of data reuse and the establishment of this practice as a norm has the potential to benefit all stakeholders in the life sciences.
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Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany
| | - Alenka Hafner
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Current Affiliation: Intercollege Graduate Degree Program in Plant Biology, Penn State University, University Park, State College, PA, United States of America
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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Yuan Z, Ye X, Zhu L, Zhang N, An Z, Zheng WJ. Virome assembly and annotation in brain tissue based on next-generation sequencing. Cancer Med 2020; 9:6776-6790. [PMID: 32738030 PMCID: PMC7520322 DOI: 10.1002/cam4.3325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/20/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022] Open
Abstract
The glioblastoma multiforme (GBM) is one of the deadliest tumors. It has been speculated that virus plays a role in GBM but the evidences are controversy. Published researches are mainly limited to studies on the presence of human cytomegalovirus (HCMV) in GBM. No comprehensive assessment of the brain virome, the collection of viral material in the brain, based on recently sequenced data has been performed. Here, we characterized the virome from 111 GBM samples and 57 normal brain samples from eight projects in the SRA database by a tested and comprehensive assembly approach. The annotation of the assembled contigs showed that most viral sequences in the brain belong to the viral family Retroviridae. In some GBM samples, we also detected full genome sequence of a novel picornavirus recently discovered in invertebrates. Unlike previous reports, our study did not detect herpes virus such as HCMV in GBM from the data we used. However, some contigs that cannot be annotated with any known genes exhibited antibody epitopes in their sequences. These findings provide several avenues for potential cancer therapy: the newly discovered picornavirus could be a starting point to engineer novel oncolytic virus; and the exhibited antibody epitopes could be a source to explore potential drug targets for immune cancer therapy. By characterizing the virosphere in GBM and normal brain at a global level, the results from this study strengthen the link between GBM and viral infection which warrants the further investigation.
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Affiliation(s)
- Zihao Yuan
- School of Biomedical InformaticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Xiaohua Ye
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Lisha Zhu
- School of Biomedical InformaticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Ningyan Zhang
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Zhiqiang An
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - W. Jim Zheng
- School of Biomedical InformaticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
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Lejal E, Estrada-Peña A, Marsot M, Cosson JF, Rué O, Mariadassou M, Midoux C, Vayssier-Taussat M, Pollet T. Taxon Appearance From Extraction and Amplification Steps Demonstrates the Value of Multiple Controls in Tick Microbiota Analysis. Front Microbiol 2020; 11:1093. [PMID: 32655509 PMCID: PMC7325928 DOI: 10.3389/fmicb.2020.01093] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 05/01/2020] [Indexed: 12/27/2022] Open
Abstract
Background The development of high-throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high-throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g., individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: homogenization, DNA extraction, and DNA amplification. Results Controls yielded a significant number of sequences (1,126-13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e., the percentage of sequences belonging to OTUs identified as contaminants) varied with tick instar and sex: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in homogenization and extraction reagent controls, highlighting the importance of carefully controlling these steps. Conclusion Here, we showed that contaminant OTUs from sample laboratory processing steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples.
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Affiliation(s)
- Emilie Lejal
- UMR BIPAR, Animal Health Laboratory, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | | | - Maud Marsot
- Laboratory for Animal Health, Epidemiology Unit, ANSES, University Paris-Est, Maisons-Alfort, France
| | - Jean-François Cosson
- UMR BIPAR, Animal Health Laboratory, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Olivier Rué
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France.,INRAE, Bioinfomics, MIGALE Bbioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mahendra Mariadassou
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France.,INRAE, Bioinfomics, MIGALE Bbioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cédric Midoux
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France.,INRAE, Bioinfomics, MIGALE Bbioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France.,INRAE, PROSE, Université Paris-Saclay, Antony, France
| | | | - Thomas Pollet
- UMR BIPAR, Animal Health Laboratory, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France.,UMR ASTRE, CIRAD, INRAE, Montpellier, France
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41
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Guizzo MG, Neupane S, Kucera M, Perner J, Frantová H, da Silva Vaz I, de Oliveira PL, Kopacek P, Zurek L. Poor Unstable Midgut Microbiome of Hard Ticks Contrasts With Abundant and Stable Monospecific Microbiome in Ovaries. Front Cell Infect Microbiol 2020; 10:211. [PMID: 32457850 PMCID: PMC7225584 DOI: 10.3389/fcimb.2020.00211] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/17/2020] [Indexed: 01/17/2023] Open
Abstract
Culture-independent metagenomic methodologies have enabled detection and identification of microorganisms in various biological systems and often revealed complex and unknown microbiomes. In many organisms, the microbiome outnumbers the host cells and greatly affects the host biology and fitness. Ticks are hematophagous ectoparasites with a wide host range. They vector a number of human and animal pathogens and also directly cause major economic losses in livestock. Although several reports on a tick midgut microbiota show a diverse bacterial community, in most cases the size of the bacterial population has not been determined. In this study, the microbiome was quantified in the midgut and ovaries of the ticks Ixodes ricinus and Rhipicephalus microplus before, during, and after blood feeding. Although the size of bacterial community in the midgut fluctuated with blood feeding, it was overall extremely low in comparison to that of other hematophagous arthropods. In addition, the tick ovarian microbiome of both tick species exceeded the midgut 16S rDNA copy numbers by several orders of magnitude. This indicates that the ratio of a tick midgut/ovary microbiome represents an exception to the general biology of other metazoans. In addition to the very low abundance, the tick midgut diversity in I. ricinus was variable and that is in contrast to that found in the tick ovary. The ovary of I. ricinus had a very low bacterial diversity and a very high and stable bacterial abundance with the dominant endosymbiont, Midichloria sp. The elucidation of this aspect of tick biology highlights a unique tissue-specific microbial-invertebrate host interaction.
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Affiliation(s)
- Melina Garcia Guizzo
- Central European Institute of Technology (CEITEC), Center for Zoonoses, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Saraswoti Neupane
- Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Matej Kucera
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czechia.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Jan Perner
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Helena Frantová
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Itabajara da Silva Vaz
- Laboratório de Imunologia Aplicada a Sanidade Animal, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pedro L de Oliveira
- Laboratório de Bioquímica de Artrópodes Hematófagos, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Petr Kopacek
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Ludek Zurek
- Central European Institute of Technology (CEITEC), Center for Zoonoses, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia.,Department of Chemistry and Biochemistry, Mendel University, Brno, Czechia
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Marcelino VR, Clausen PTLC, Buchmann JP, Wille M, Iredell JR, Meyer W, Lund O, Sorrell TC, Holmes EC. CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data. Genome Biol 2020; 21:103. [PMID: 32345331 PMCID: PMC7189439 DOI: 10.1186/s13059-020-02014-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 04/13/2020] [Indexed: 01/19/2023] Open
Abstract
There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. The pipeline substantially outperforms other commonly used software in identifying bacteria and fungi and can efficiently use the entire NCBI nucleotide collection as a reference to detect species with incomplete genome data from all biological kingdoms. CCMetagen is user-friendly, and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
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Affiliation(s)
- Vanessa R Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia.
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia.
- School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Philip T L C Clausen
- National Food Institute, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Jan P Buchmann
- School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Jonathan R Iredell
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, 2145, Australia
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, 2145, Australia
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Ole Lund
- National Food Institute, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
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Chronic Corynebacterium striatum Septic Arthritis in a Patient Referred for Total Knee Arthroplasty. Case Rep Orthop 2020; 2020:1392182. [PMID: 32206362 PMCID: PMC7077040 DOI: 10.1155/2020/1392182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/25/2020] [Indexed: 11/24/2022] Open
Abstract
Background While Corynebacterium striatum and other Corynebacterium species were historically considered contaminants, they are recently being identified as pathogens with increasing frequency. Case Summary. We report the case of a 78-year-old gentleman with a three-year history of knee pain and established diagnosis of osteoarthritis referred for consideration for total knee arthroplasty. He had no knee pain with passive range-of-motion. Plain films demonstrated bony erosions atypical for osteoarthritis. Joint aspiration white blood cell count was 30,548/mm3, but multiple cultures were positive for C. striatum. The infection was successfully treated with open irrigation and debridement, complete synovectomy, and six weeks of intravenous daptomycin. Conclusion To our knowledge, this is the first report of chronic C. striatum septic arthritis of a native joint and only the third case of C. striatum septic arthritis of the knee.C. striatum. The infection was successfully treated with open irrigation and debridement, complete synovectomy, and six weeks of intravenous daptomycin. C. striatum. The infection was successfully treated with open irrigation and debridement, complete synovectomy, and six weeks of intravenous daptomycin.
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Swanson GM, Moskovtsev S, Librach C, Pilsner JR, Goodrich R, Krawetz SA. What human sperm RNA-Seq tells us about the microbiome. J Assist Reprod Genet 2020; 37:359-368. [PMID: 31902104 PMCID: PMC7056791 DOI: 10.1007/s10815-019-01672-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/19/2019] [Indexed: 10/25/2022] Open
Abstract
PURPOSE The study was designed to assess the capacity of human sperm RNA-seq data to gauge the diversity of the associated microbiome within the ejaculate. METHODS Semen samples were collected, and semen parameters evaluated at time of collection. Sperm RNA was isolated and subjected to RNA-seq. Microbial composition was determined by aligning sequencing reads not mapped to the human genome to the NCBI RefSeq bacterial, viral and archaeal genomes following RNA-Seq. Analysis of microbial assignments utilized phyloseq and vegan. RESULTS Microbial composition within each sample was characterized as a function of microbial associated RNAs. Bacteria known to be associated with the male reproductive tract were present at similar levels in all samples representing 11 genera from four phyla with one exception, an outlier. Shannon diversity index (p < 0.001) and beta diversity (unweighted UniFrac distances, p = 9.99e-4; beta dispersion, p = 0.006) indicated the outlier was significantly different from all other samples. The outlier sample exhibited a dramatic increase in Streptococcus. Multiple testing indicated two operational taxonomic units, S. agalactiae and S. dysgalactiae (p = 0.009), were present. CONCLUSION These results provide a first look at the microbiome as a component of human sperm RNA sequencing that has sufficient sensitivity to identify contamination or potential pathogenic bacterial colonization at least among the known contributors.
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Affiliation(s)
- Grace M Swanson
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48202, USA
| | | | | | - J Richard Pilsner
- Department of Environmental Health Sciences, University of Massachusetts Amherst School of Public Health and Health Sciences, Amherst, MA, 01003, USA
| | - Robert Goodrich
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48202, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48202, USA.
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45
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Kidd SE, Chen SCA, Meyer W, Halliday CL. A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready? Front Microbiol 2020; 10:2903. [PMID: 31993022 PMCID: PMC6971168 DOI: 10.3389/fmicb.2019.02903] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.
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Affiliation(s)
- Sarah E. Kidd
- National Mycology Reference Centre, Microbiology and Infectious Diseases, South Australia Pathology, Adelaide, SA, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Research and Education Network, Westmead Hospital, Westmead, NSW, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
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Deng X, Achari A, Federman S, Yu G, Somasekar S, Bártolo I, Yagi S, Mbala-Kingebeni P, Kapetshi J, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Ahmed AA, Ganesh V, Tamhankar M, Patterson JL, Ndembi N, Mbanya D, Kaptue L, McArthur C, Muñoz-Medina JE, Gonzalez-Bonilla CR, López S, Arias CF, Arevalo S, Miller S, Stone M, Busch M, Hsieh K, Messenger S, Wadford DA, Rodgers M, Cloherty G, Faria NR, Thézé J, Pybus OG, Neto Z, Morais J, Taveira N, R Hackett J, Chiu CY. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol 2020; 5:443-454. [PMID: 31932713 PMCID: PMC7047537 DOI: 10.1038/s41564-019-0637-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 11/08/2019] [Indexed: 12/27/2022]
Abstract
Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use. This study describes a new method that improves the sensitivity of viral detection compared with next-generation sequencing and enables the detection of emerging flaviviruses not specifically targeted a priori. Metagenomic sequencing with spiked primer enrichment is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making it applicable for diagnostic laboratory and field use.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Asmeeta Achari
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Inês Bártolo
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Shigeo Yagi
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | - Jimmy Kapetshi
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Asim A Ahmed
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Vijay Ganesh
- Massachussetts General Hospital, Boston, MA, USA
| | - Manasi Tamhankar
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Nicaise Ndembi
- Institute for Human Virology Nigeria, Abuja, Nigeria.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dora Mbanya
- Universite de Yaoundé I, Yaoundé, Cameroon.,University of Bamenda, Bamenda, Cameroon
| | | | | | | | | | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Kristina Hsieh
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Sharon Messenger
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Zoraima Neto
- Angolan National Institute of Health Research, Luanda, Angola
| | - Joana Morais
- Angolan National Institute of Health Research, Luanda, Angola
| | - Nuno Taveira
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal.,Instituto Universitário Egas Moniz (IUEM), Monte de Caparica, Portugal
| | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. .,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. .,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
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Ji P, Aw TG, Van Bonn W, Rose JB. Evaluation of a portable nanopore-based sequencer for detection of viruses in water. J Virol Methods 2019; 278:113805. [PMID: 31891731 DOI: 10.1016/j.jviromet.2019.113805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]
Abstract
The newly emerged nanopore sequencing technology such as MinION™ allows for real-time detection of long DNA/RNA fragments on a portable device, yet few have examined its performance for environmental viromes. Here we seeded one RNA virus bacteriophage MS2 and one DNA virus bacteriophage PhiX174 into 10 L well water at three levels ranging from 1 to 21,100 plaque-forming units (PFU)/mL. Two workflows were established to maximize the number of sequencing reads of RNA and DNA viruses using MinION™. With dead-end ultrafiltration, PEG precipitation, and random amplification, MinION™ was capable of detecting MS2 at 155 PFU/mL and PhiX174 at 1-2 PFU/mL. While the DNA workflow only detected PhiX174, the RNA workflow detected both MS2 and PhiX174. The virus concentration, or relative abundance of viral nucleic acids in total nucleic acids, is critical to the proportion of viral reads in sequencing results. Our findings also highlight the importance of including control samples in sequencing runs for environmental water samples with low virus abundance.
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Affiliation(s)
- Pan Ji
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - William Van Bonn
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA; A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL 60605, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA.
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48
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MinION sequencing of Streptococcus suis allows for functional characterization of bacteria by multilocus sequence typing and antimicrobial resistance profiling. J Microbiol Methods 2019; 169:105817. [PMID: 31881288 DOI: 10.1016/j.mimet.2019.105817] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 01/31/2023]
Abstract
In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information. The Oxford Nanopore MinION sequencer has unparalleled potential as a rapid disease diagnostic tool due to its high mobility, accessibility, and short turnaround time. However, there is a lack of rigorous quality assessment and control processes standardizing the testing on the MinION, which is necessary for incorporation into a diagnostic workflow. Thus, our study examined the use of the MinION sequencer for bacterial whole genome generation and characterization. Using Streptococcus suis as a model, we optimized DNA isolation and treatments to be used for MinION sequencing and standardized de novo assembly to quickly generate a full-length consensus sequence achieving a 99.4% average accuracy. The consensus genomes from MinION sequencing were able to accurately predict the multilocus sequence type in 8 out of 10 samples and identified antimicrobial resistance profiles for 100% of the samples, despite the concern of a high error rate. The inability to unequivocally predict sequence types was due to difficulty in differentiating high identity alleles, which was overcome by applying additional error correction methods to increase consensus accuracy. This manuscript provides methods for the use of MinION sequencing for identification of S. suis genome sequence, sequence type, and antibiotic resistance profile that can be used as a framework for identification and classification of other pathogens.
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49
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De Simone G, Pasquadibisceglie A, Proietto R, Polticelli F, Aime S, J M Op den Camp H, Ascenzi P. Contaminations in (meta)genome data: An open issue for the scientific community. IUBMB Life 2019; 72:698-705. [PMID: 31869003 DOI: 10.1002/iub.2216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 11/30/2019] [Indexed: 12/13/2022]
Abstract
In recent years, the high throughput and the low cost of next-generation sequencing (NGS) technologies have led to an increase of the amount of (meta)genomic data, revolutionizing genomic research studies. However, the quality of sequencing data could be affected by experimental errors derived from defective methods and protocols. This represents a serious problem for the scientific community with a negative impact on the correctness of studies that involve genomic sequence analysis. As a countermeasure, several alignment and taxonomic classification tools have been developed to uncover and correct errors. In this critical review some of these integrated software tools and pipelines used to detect contaminations in reference genome databases and sequenced samples are reported. In particular, case studies of bacterial contaminations, contaminations of human origin, mitochondrial contaminations of ancient DNA, and cross contaminations are examined.
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Affiliation(s)
| | | | | | | | - Silvio Aime
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, The Netherlands
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Roma, Italy
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50
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Quintana JF, Kumar S, Ivens A, Chow FWN, Hoy AM, Fulton A, Dickinson P, Martin C, Taylor M, Babayan SA, Buck AH. Comparative analysis of small RNAs released by the filarial nematode Litomosoides sigmodontis in vitro and in vivo. PLoS Negl Trop Dis 2019; 13:e0007811. [PMID: 31770367 PMCID: PMC6903752 DOI: 10.1371/journal.pntd.0007811] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/10/2019] [Accepted: 09/26/2019] [Indexed: 12/13/2022] Open
Abstract
Background The release of small non-coding RNAs (sRNAs) has been reported in parasitic nematodes, trematodes and cestodes of medical and veterinary importance. However, little is known regarding the diversity and composition of sRNAs released by different lifecycle stages and the portion of sRNAs that persist in host tissues during filarial infection. This information is relevant to understanding potential roles of sRNAs in parasite-to-host communication, as well as to inform on the location within the host and time point at which they can be detected. Methodology and principal findings We have used small RNA (sRNA) sequencing analysis to identify sRNAs in replicate samples of the excretory-secretory (ES) products of developmental stages of the filarial nematode Litomosoides sigmodontis in vitro and compare this to the parasite-derived sRNA detected in host tissues. We show that all L. sigmodontis developmental stages release RNAs in vitro, including ribosomal RNA fragments, 5’-derived tRNA fragments (5’-tRFs) and, to a lesser extent, microRNAs (miRNAs). The gravid adult females (gAF) produce the largest diversity and abundance of miRNAs in the ES compared to the adult males or microfilariae. Analysis of sRNAs detected in serum and macrophages from infected animals reveals that parasite miRNAs are preferentially detected in vivo, compared to their low levels in the ES products, and identifies miR-92-3p and miR-71-5p as L. sigmodontis miRNAs that are stably detected in host cells in vivo. Conclusions Our results suggest that gravid adult female worms secrete the largest diversity of extracellular sRNAs compared to adult males or microfilariae. We further show differences in the parasite sRNA biotype distribution detected in vitro versus in vivo. We identify macrophages as one reservoir for parasite sRNA during infection, and confirm the presence of parasite miRNAs and tRNAs in host serum during patent infection. Lymphatic and visceral filariasis, as well as loiasis and onchocerciasis, are parasitic infections caused by filarial nematodes that can cause extensive and diverse clinical manifestations, including edemas of the lower limbs and visual impairment. These parasites successfully maintain a crosstalk with the immune system of their host and one potential mediator of this communication is extracellular small non-coding RNAs (sRNAs) released by the parasite. However, little is known of the mechanisms of sRNA export, how the exported sRNAs differ between lifecycle stages, and how the parasite microenvironment (e.g. in vitro vs. in vivo) contributes to the composition of sRNAs that can be detected. In this report, we show that all the developmental stages of the filarial parasite Litomosoides sigmodontis release sRNAs, which include tRNA fragments and miRNAs, in vitro. A subset of the miRNAs are differentially represented in the ES products between adult stages (males and gravid females) and larval stages (microfilariae) in vitro, however all of the miRNAs detected in serum or macrophages in vivo are present in the ES from all life stages. We show that the parasite-derived miRNAs are protected from degradation in vitro and are stable in vivo, as they are readily detectable in the serum of infected jirds. Several parasite miRNAs are also detected within macrophages purified from infected hosts, consistent with parasite RNAs having a yet unidentified functional role in host cells.
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Affiliation(s)
- Juan F. Quintana
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sujai Kumar
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alasdair Ivens
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Franklin W. N. Chow
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna M. Hoy
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison Fulton
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Dickinson
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Coralie Martin
- Unite Molecules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Sorbonne Universites, Museum national d’Histoire naturelle, CNRS, CP52, Paris, France
| | - Matthew Taylor
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon A. Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Amy H. Buck
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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