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Andreo-Martínez P, García-Martínez N, Sánchez-Samper EP, Martínez-González AE. An approach to gut microbiota profile in children with autism spectrum disorder. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:115-135. [PMID: 31713352 DOI: 10.1111/1758-2229.12810] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/04/2019] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
In recent years, there has been an increase in studies on the implications of gut microbiota (GM) on the behaviour of children with autism spectrum disorders (ASD) due to a dysbiosis in GM that can trigger onset, development or progression of ASD through the microbiota-gut-brain axis. The aim of this study is to carry out a systematic review of articles from the last 6 years that analyse GM in children with ASD compared to GM in control groups. Children with ASD showed a higher abundance of Roseburia and Candida genera, and lower abundance of Dialister, Bilophila, Veillonella, Streptococcus, Coprococcus and Prevotella genera. Those differences can be attributed to factors such as different nationalities, nature of control groups, place where the sample was taken, gastrointestinal (GI) problems or bacterial detection methods. It is still too early to define a specific GM profile of children with ASD, and future studies should focus on homogenizing the characteristics of samples and control groups. Furthermore, new multicentre studies should also focus on the impact of GM on GI physiology, neurophysiology and behaviour of children with ASD, and on performing psychometric analyses of the correlation between the severity of ASD behavioural symptoms and GM profiles.
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Affiliation(s)
- Pedro Andreo-Martínez
- Department of Agricultural Chemistry, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Murcia, 30100, Spain
- Department of Chemical Engineering, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Murcia, 30100, Spain
| | - Nuria García-Martínez
- Department of Agricultural Chemistry, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Murcia, 30100, Spain
| | - Elvira Pilar Sánchez-Samper
- Research Group of Human Nutrition and Food Sciences (NUTBRO), Veterinary Faculty, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Murcia, Spain
- Murcian Institute of Biosanitary Research Virgen de la Arrixaca (IMIB), AREA 3, Digestive and Endocrine-Metabolic Diseases, Nutrition Research Line, Murcia, Spain
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Stebner A, Ensser A, Geißdörfer W, Bozhkov Y, Lang R. Molecular diagnosis of polymicrobial brain abscesses with 16S-rDNA-based next-generation sequencing. Clin Microbiol Infect 2020; 27:76-82. [PMID: 32244052 DOI: 10.1016/j.cmi.2020.03.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Brain abscesses lead to high mortality despite antibiotic and surgical treatment. Identification of causative bacteria is important to guide antibiotic therapy, but culture-based methods and molecular diagnostics by Sanger sequencing of 16S PCR products are hampered by antibiotic treatment and the often polymicrobial nature of brain abscesses. We have applied 16S-rRNA-based next-generation sequencing (NGS) for metagenomic analysis of intracranial abscess (brain and epidural) and meningitis samples. METHODS Seventy-nine samples from 54 patients with intracranial abscesses or meningitis were included. DNA was subjected to 16S PCR. Amplicons were analysed with the Illumina MiSeq system, sequence reads were blasted versus the NCBI 16S bacterial database and analysed using MEGAN software. Results were compared to those of gram-staining, culture and Sanger sequencing. RESULTS The NGS workflow was successful for 51 intracranial abscesses (46 brain and five epidural) and nine meningitis samples. Inclusion of (mono)bacterial meningitis samples allowed us to establish a cut-off criterion for the exclusion of contaminating sequences. In total 86 bacterial taxa were identified in brain abscesses by NGS, with Streptococcus intermedius and Fusobacterium nucleatum as most prevalent species; Propionibacterium and Staphylococcus spp. were associated with epidural abscesses. NGS identified two or more bacterial taxa in 31/51 intracranial abscesses, revealing the polymicrobial nature of these infections and allowing the discrimination of up to 16 bacterial taxa per sample. CONCLUSION These results extend earlier studies showing that NGS methods expand the spectrum of bacteria detected in brain abscesses and demonstrate that the MiSeq platform is suitable for metagenomic diagnostics of this severe infection.
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Affiliation(s)
- A Stebner
- Institut für Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - A Ensser
- Virologisches Institut, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - W Geißdörfer
- Institut für Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Y Bozhkov
- Neurochirurgische Klinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - R Lang
- Institut für Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany.
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Cummings LA, Hoogestraat DR, Rassoulian-Barrett SL, Rosenthal CA, Salipante SJ, Cookson BT, Hoffman NG. Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture. Sci Rep 2020; 10:5446. [PMID: 32214207 PMCID: PMC7096443 DOI: 10.1038/s41598-020-62424-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/11/2020] [Indexed: 01/19/2023] Open
Abstract
Optimal clinical decision-making depends on identification of clinically relevant organisms present in a sample. Standard microbiological culture may fail to identify unusual or fastidious organisms and can misrepresent relative abundance of sample constituents. Culture-independent methods have improved our ability to deconvolute polymicrobial patient samples. We used next-generation 16S rRNA gene sequencing (NGS16S) to determine how often cultivatable organisms in complex polymicrobial samples are not reported by standard culture. Twenty consecutive bronchoalveolar lavage (BAL) samples were plated to standard and additional media; bacteria were identified by NGS16S analysis of DNA extracted directly from samples or from washed culture plates. 96% of organisms identified were cultivable, but only 21% were reported by standard culture, indicating that standard work-up provides an incomplete assessment of microbial constituents. Direct NGS16S correlated well with standard culture, identifying the same predominant organism in 50% of samples. When predominant organisms differed, NGS16S most often detected anaerobes, whose growth is unsupported by standard culture conditions for this specimen. NGS16S identified more organisms per sample and allowed identification of fastidious organisms, while culture was better at capturing organisms when bacterial load was low, and allowed incidental recovery of non-bacterial pathogens. Molecular and culture-based methods together detect more organisms than either method alone.
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Affiliation(s)
- Lisa A Cummings
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Daniel R Hoogestraat
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | | | | | - Stephen J Salipante
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Brad T Cookson
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA.,Departments of Microbiology, University of Washington, Seattle, Washington, USA
| | - Noah G Hoffman
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
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54
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Soil properties influence bacterial abundance and diversity under different land-use regimes in semi-arid environments. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2019.e00246] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Ung L, Bispo PJM, Doan T, Van Gelder RN, Gilmore MS, Lietman T, Margolis TP, Zegans ME, Lee CS, Chodosh J. Clinical metagenomics for infectious corneal ulcers: Rags to riches? Ocul Surf 2020; 18:1-12. [PMID: 31669750 PMCID: PMC9837861 DOI: 10.1016/j.jtos.2019.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 01/17/2023]
Abstract
The emergence of clinical metagenomics as an unbiased, hypothesis-free approach to diagnostic testing is set to fundamentally alter the way infectious diseases are detected. Long envisioned as the solution to the limitations of culture-based conventional microbiology, next generation sequencing methods will soon mature, and our attention will inevitably turn to how they can be applied to areas of medicine which need it most urgently. In ophthalmology, the demand for this technology is particularly pressing for the care of infectious corneal ulcers, where current diagnostic tests may fail to identify a causative organism in over half of cases. However, the optimism found in the budding discourse surrounding clinical metagenomics belies the reality that clinicians and scientists will soon be inundated by oppressive volumes of sequencing data, much of which will be foreign and unfamiliar. Therefore, our success in translating clinical metagenomics is likely to hinge on how we make sense of these data, and understanding its implications for the interpretation and implementation of sequencing into routine clinical care. In this consortium-led review, we provide an outline of these data-related issues and how they may be used to inform technical workflows, with the hope that we may edge closer to realizing the potential of clinical metagenomics for this important unmet need.
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Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Paulo J M Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | | | - Michael S Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thomas Lietman
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Todd P Margolis
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in Saint Louis, Saint Louis, USA
| | - Michael E Zegans
- Department of Surgery (Ophthalmology), and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Cecilia S Lee
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
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Winand R, Bogaerts B, Hoffman S, Lefevre L, Delvoye M, Van Braekel J, Fu Q, Roosens NHC, De Keersmaecker SCJ, Vanneste K. TARGETING THE 16S RRNA GENE FOR BACTERIAL IDENTIFICATION IN COMPLEX MIXED SAMPLES: COMPARATIVE EVALUATION OF SECOND (ILLUMINA) AND THIRD (OXFORD NANOPORE TECHNOLOGIES) GENERATION SEQUENCING TECHNOLOGIES. Int J Mol Sci 2019; 21:ijms21010298. [PMID: 31906254 PMCID: PMC6982111 DOI: 10.3390/ijms21010298] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
Rapid, accurate bacterial identification in biological samples is an important task for microbiology laboratories, for which 16S~rRNA gene Sanger sequencing of cultured isolates is frequently used. In contrast, next-generation sequencing does not require intermediate culturing steps and can be directly applied on communities, but its performance has not been extensively evaluated. We present a comparative evaluation of second (Illumina) and third (Oxford Nanopore Technologies (ONT)) generation sequencing technologies for 16S targeted genomics using a well-characterized reference sample. Different 16S gene regions were amplified and sequenced using the Illumina MiSeq, and analyzed with Mothur. Correct classification was variable, depending on the region amplified. Using a majority vote over all regions, most false positives could be eliminated at the genus level but not the species level. Alternatively, the entire 16S gene was amplified and sequenced using the ONT MinION, and analyzed with Mothur, EPI2ME, and GraphMap. Although >99\% of reads were correctly classified at the genus level, up to $\approx$40\% were misclassified at the species level. Both~technologies, therefore, allow reliable identification of bacterial genera, but can potentially misguide identification of bacterial species, and constitute viable alternatives to Sanger sequencing for rapid analysis of mixed samples without requiring any culturing steps.
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Ramachandran V, Haruno LS, Browne TS, Woc-Colburn LE, Rosenfeld SB, Shenava VR. Chronic Osteomyelitis Caused by Haemophilus parainfluenzae: A Case Report. JBJS Case Connect 2019; 8:e20. [PMID: 29595537 DOI: 10.2106/jbjs.cc.17.00144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CASE A 14-year-old boy presented with a pathologic fracture of the distal aspect of the tibia and a remote history of a dog bite near the injury site. Imaging studies, biopsy, and presentation corroborated the diagnosis of chronic osteomyelitis. Multiple diagnostic methods were negative until an open biopsy identified Haemophilus parainfluenzae, a fastidious oropharyngeal bacterium, with polymerase chain reaction analysis. The patient underwent extensive debridement, placement of external fixation, and a year-long antibiotic therapy regimen. He subsequently required a tibial-fibular osteotomy at a second site with placement of an intramedullary nail for correction of a leg-length discrepancy. CONCLUSION This case report illustrates the complex management of chronic osteomyelitis in pediatric patients, its sequelae, and the importance of considering treatment of atypical pathogens.
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Affiliation(s)
| | - Lee S Haruno
- Division of Orthopedic Surgery, Texas Children's Hospital, Houston, Texas
| | - Theodora S Browne
- Division of Orthopedic Surgery, Texas Children's Hospital, Houston, Texas
| | - Laila E Woc-Colburn
- Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Scott B Rosenfeld
- Division of Orthopedic Surgery, Texas Children's Hospital, Houston, Texas
| | - Vinitha R Shenava
- Division of Orthopedic Surgery, Texas Children's Hospital, Houston, Texas
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Alawi M, Burkhardt L, Indenbirken D, Reumann K, Christopeit M, Kröger N, Lütgehetmann M, Aepfelbacher M, Fischer N, Grundhoff A. DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples. Sci Rep 2019; 9:16841. [PMID: 31727957 PMCID: PMC6856179 DOI: 10.1038/s41598-019-52881-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
We describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate that DAMIAN rapidly identifies pathogens in different diagnostic entities, and accurately classifies viral agents down to the strain level. We furthermore show that DAMIAN is able to assemble full-length viral genomes even in samples co-infected with multiple virus strains, an ability which is of considerable advantage for the investigation of outbreak scenarios. While DAMIAN, similar to other pipelines, analyzes single samples to perform classification of sequences according to their likely taxonomic origin, it also includes a tool for cohort-based analysis. This tool uses cross-sample comparisons to identify sequence signatures that are frequently present in a sample group of interest (e.g., a disease-associated cohort), but occur less frequently in control cohorts. As this approach does not require homology searches in databases, it principally allows the identification of not only known, but also completely novel pathogens. Using samples from a meningitis outbreak, we demonstrate the feasibility of this approach in identifying enterovirus as the causative agent.
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Affiliation(s)
- Malik Alawi
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany.,Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lia Burkhardt
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Kerstin Reumann
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Maximilian Christopeit
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. .,German Center for Infection Research, DZIF, partner site Hamburg-Borstel-Lübeck-Riems, Germany.
| | - Adam Grundhoff
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany. .,German Center for Infection Research, DZIF, partner site Hamburg-Borstel-Lübeck-Riems, Germany.
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Winston McPherson G, Long T, Salipante SJ, Rongitsch JA, Hoffman NG, Stephens K, Penewit K, Greene DN. The Vaginal Microbiome of Transgender Men. Clin Chem 2019; 65:199-207. [PMID: 30602481 DOI: 10.1373/clinchem.2018.293654] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/16/2018] [Indexed: 01/28/2023]
Abstract
BACKGROUND Hormonal changes influence the composition of vaginal flora, which is directly related to the health of an individual. Transgender men prescribed testosterone experience a vaginal hormone composition that differs from cisgender women. To the author's knowledge, there are no clinical studies evaluating the influence that testosterone administration has on the vaginal microbiome. METHODS Vaginal swabs were self-collected by a cohort of self-identified healthy transgender men prescribed testosterone for at least 1 year (n = 28) and from cisgender women who were used as the comparator (n = 8). Participants completed a questionnaire to indicate the mode and dose of testosterone administration, sexual history, and vaginal health. Serum was collected for hormone analysis. Bacterial community profiles were assessed with broad-range PCR primers targeting the V3-V4 hypervariable region of the 16S bacterial rRNA, next-generation sequencing, and analysis by phylogenetic placement. RESULTS Compared to cisgender women, the vaginal floras of transgender men were less likely to have Lactobacillus as their primary genus. Intravaginal estrogen administration was positively associated with the presence of Lactobacillus in transgender men (P = 0.045). Transgender men had a significantly increased relative abundance of >30 species and a significantly higher α diversity (P = 0.0003). The presence of Lactobacillus was significantly associated with a lower α diversity index (P = 0.017). CONCLUSIONS The vaginal microbiome of transgender men who were assigned a female sex at birth and use testosterone may differ from that of cisgender women. Intravaginal estrogen administration may reduce these differences by promoting colonization with Lactobacillus species and decreasing α diversity.
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Affiliation(s)
| | - Thomas Long
- University of Washington, Department of Laboratory Medicine, Seattle, WA
| | | | | | - Noah G Hoffman
- University of Washington, Department of Laboratory Medicine, Seattle, WA
| | - Karen Stephens
- University of Washington, Department of Laboratory Medicine, Seattle, WA
| | - Kelsi Penewit
- University of Washington, Department of Laboratory Medicine, Seattle, WA
| | - Dina N Greene
- University of Washington, Department of Laboratory Medicine, Seattle, WA;
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Rapid diagnosis of bacterial meningitis by nanopore 16S amplicon sequencing: A pilot study. Int J Med Microbiol 2019; 309:151338. [PMID: 31444101 DOI: 10.1016/j.ijmm.2019.151338] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/20/2019] [Accepted: 08/10/2019] [Indexed: 12/13/2022] Open
Abstract
Early administration of antibiotics is crucial in the management of bacterial meningitis. Rapid pathogen identification helps to make a definite diagnosis of bacterial meningitis and enables tailored antibiotic treatment. We investigated if the 16S amplicon sequencing performed by MinION, a nanopore sequencer, was capable of rapid pathogen identification in bacterial meningitis. Six retrospective cases of confirmed bacterial meningitis and two prospective cases were included. The initial cerebrospinal fluid (CSF) samples of these patients were used for the experiments. DNA was extracted from the CSF, and PCR was performed on the 16S ribosomal DNA (16S rDNA). Sequencing libraries were prepared using the PCR products, and MinION sequencing was performed for up to 3 h. The reads were aligned to the bacterial database, and the results were compared to the conventional culture studies. Pathogenic bacteria were successfully detected from the CSF by 16S sequencing in all retrospective cases. 16S amplicon sequencing was more sensitive than conventional diagnostic tests and worked properly even in antibiotics-treated samples. MinION sequencing significantly reduced the turnaround time, and even 10 min of sequencing was sufficient for pathogen detection in certain cases. Protocol adjustment could further increase the sensitivity and reduce the turnaround time for MinION sequencing. Finally, the prospective application of MinION 16S sequencing was successful. Nanopore 16S amplicon sequencing is capable of rapid bacterial identification from the CSF of the bacterial meningitis patients. It may have many advantages over conventional diagnostic tests and should therefore be applied in a larger number of patients in the future.
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Broad-range PCR Application in a Large Academic Pediatric Center: Clinical Value and Challenges in Diagnosis of Infectious Diseases. Pediatr Infect Dis J 2019; 38:786-790. [PMID: 30920482 DOI: 10.1097/inf.0000000000002308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Broad-range polymerase chain reaction (BR-PCR) detects infectious pathogens from clinical specimens using targets for bacteria (16S rRNA), fungi (28S rDNA), and mycobacteria (fluorescence resonance energy transfer and heat shock protein 65 gene) with reported diagnostic sensitivity and specificity ranging from 43% to 100% and 100%, respectively. We describe our experience when applying BR-PCR to clinical samples submitted for conventional infectious disease testing [conventional testing (CT)] from pediatric patients with concern for infection. METHODS Retrospective analysis of clinical samples obtained from Nationwide Children's Hospital microbiology laboratory from January 2011 to December 2014 and sent for BR-PCR. Medical record review collected data on patient characteristics, clinical manifestations, laboratory results and antimicrobials prescribed, and a determination of clinical value of BR-PCR was assigned. RESULTS There were 247 clinical samples from 163 patients identified; 71 (44%) patients were immunocompromised and 192 (78%) samples reflected pretreatment with antimicrobials. A clinically significant putative organism was identified for 59 samples (24%) between all diagnostic modalities. Conventional testing identified organisms in 41 (17%) samples, 17 of which were corroborated by BR-PCR. Broad-range polymerase chain reaction identified an organism in an additional 18 samples with negative CT results and was considered to provide additional important clinical information. Broad-range polymerase chain reaction detected a bacterial or fungal organism more frequently from tissue samples than from bronchoalveolar lavage or other fluid samples (P = 0.0096, χ). CONCLUSIONS In our cohort, BR-PCR was an important adjunctive diagnostic in identifying bacteria and fungi in complex clinical situations. Additional data are needed to define the optimal clinical circumstances and specimen type in which BR-PCR can provide the highest diagnostic yield.
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Martínez-González AE, Andreo-Martínez P. The Role of Gut Microbiota in Gastrointestinal Symptoms of Children with ASD. MEDICINA (KAUNAS, LITHUANIA) 2019; 55:E408. [PMID: 31357482 PMCID: PMC6722942 DOI: 10.3390/medicina55080408] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/27/2022]
Abstract
Background and objectives: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired communication, social interaction disorder, and repetitive behavior. Dysbiotic gut microbiota (GM) could be a contributing factor to the appearance of ASD, as gastrointestinal (GI) symptoms are comorbidities frequently reported in ASD. As there is a lack of reviews about the role played by GM in the GI symptoms of ASD, this work aimed to carry out a systematic review of current studies comparing the GM of children with ASD and GI symptoms with those of healthy controls in the last six years. Materials and Methods: The systematic review was performed following the PRISMA guidelines. The databases chosen were Web of Science, Scopus, PubMed, and PsycINFO, and the keywords were (gut* OR intestine* OR bowel* OR gastrointestinal*) AND (microbiota* OR microflora* OR bacteria* OR microbiome* OR flora* OR bacterial* OR bacteria* OR microorganism* OR feces* OR stool*) AND (autistic* OR autism* OR ASD*). Results: A total of 16 articles were included. Ten articles performed correlations analysis between GI symptoms and ASD. Among those 10 articles, 7 found differences between the GI symptoms present in children with ASD and healthy controls. The most common GI symptom was constipation. Among the seven articles that found differences, three performed correlations analysis between GI symptoms and gut microbe abundance. Candida, Prevotella, Streptococcus, and Veillonella showed higher and lower abundance, respectively, in children with ASD and GI symptoms in more than one article. Bacteroidetes, Firmicutes, Actinomyces, Dorea, Lactobacillus, Faecalibacterium prausnitzii, and Bacteroidetes/Firmicutes ratios showed abundance discrepancies. Conclusions: It is still too early to draw a conclusion about the gut microbes involved in GI symptoms of ASD. Future research should consider the relationship between ASD behavior, GM, and GI symptoms in a multidisciplinary way and homogenize sample characteristics.
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Affiliation(s)
| | - Pedro Andreo-Martínez
- Department of Agricultural Chemistry, Faculty of Chemistry, University of Murcia, Campus of Espinardo, 30100 Murcia, Spain.
- Department of Chemical Engineering, Faculty of Chemistry, University of Murcia, Campus of Espinardo, 30100 Murcia, Spain.
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Song D, Liu H, Ji H, Lei Y. Whole Slide Imaging for High-Throughput Sensing Antibiotic Resistance at Single-Bacterium Level and Its Application to Rapid Antibiotic Susceptibility Testing. Molecules 2019; 24:molecules24132441. [PMID: 31277201 PMCID: PMC6651422 DOI: 10.3390/molecules24132441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 01/01/2023] Open
Abstract
Since conventional culture-based antibiotic susceptibility testing (AST) methods are too time-consuming (typically 24–72 h), rapid AST is urgently needed for preventing the increasing emergence and spread of antibiotic resistant infections. Although several phenotypic antibiotic resistance sensing modalities are able to reduce the AST time to a few hours or less, concerning the biological heterogeneity, their accuracy or limit of detection are limited by low throughput. Here, we present a rapid AST method based on whole slide imaging (WSI)-enabled high-throughput sensing antibiotic resistance at single-bacterium level. The time for determining the minimum inhibitory concentration (MIC) was theoretically shortest, which ensures that the growth of each individual cell present in a large population is inhibited. As a demonstration, our technique was able to sense the growth of at least several thousand bacteria at single-cell level. Reliable MIC of Enterobacter cloacae against gentamicin was obtained within 1 h, while the gold standard broth dilution method required at least 16 h for the same result. In addition, the application of our method prevails over other imaging-based AST approaches in allowing rapid and accurate determination of antibiotic susceptibility for phenotypically heterogeneous samples, in which the number of antibiotic resistant cells was negligible compared to that of the susceptible cells. Hence, our method shows great promise for both rapid AST determination and point-of-care testing of complex clinical bacteria isolates.
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Affiliation(s)
- Donghui Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Haomin Liu
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Huayi Ji
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Yu Lei
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA.
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Culbreath K, Melanson S, Gale J, Baker J, Li F, Saebo O, Kommedal O, Contreras D, Garner OB, Yang S. Validation and Retrospective Clinical Evaluation of a Quantitative 16S rRNA Gene Metagenomic Sequencing Assay for Bacterial Pathogen Detection in Body Fluids. J Mol Diagn 2019; 21:913-923. [PMID: 31229651 DOI: 10.1016/j.jmoldx.2019.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/03/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing-based 16S rRNA gene metagenomic sequencing (16S MG) technology has tremendous potential for improving diagnosis of bacterial infections given its quantitative capability and culture-independent approach. We validated and used a quantitative 16S MG assay to identify and quantify bacterial species in clinical samples from a wide spectrum of infections, including meningitis, septic arthritis, brain abscess, intra-abdominal abscess, soft tissue abscess, and pneumonia. Twenty clinical samples were tested, and 16S MG identified a total of 34 species, compared with 22 species and three descriptive findings identified by culture. 16S MG results matched culture results in 75% (15/20) of the samples but detected at least one more species in five samples, including one culture-negative cerebrospinal fluid sample that was found to contain Streptococcus intermedius. Shotgun metagenomic sequencing verified the presence of all additional species. The 16S MG assay is highly sensitive, with a limit of detection of 10 to 100 colony-forming units/mL. Other performance characteristics, including linearity, precision, and specificity, all met the requirements for a clinical test. This assay showed the advantages of accurate identification and quantification of bacteria in culture-negative and polymicrobial infections for which conventional microbiology methods are limited. It also showed promises to serve unmet clinical needs for solving difficult infectious diseases cases.
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Affiliation(s)
- Karissa Culbreath
- Department of Pathlogy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico; TriCore Reference Laboratories, Albuquerque, New Mexico
| | | | - James Gale
- TriCore Reference Laboratories, Albuquerque, New Mexico
| | - Justin Baker
- TriCore Reference Laboratories, Albuquerque, New Mexico
| | - Fan Li
- Department of Pediatrics, University of California Los Angeles, Los Angeles, California
| | | | - Oyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Deisy Contreras
- Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Omai B Garner
- Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Shangxin Yang
- Department of Pathlogy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico; Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California.
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Abstract
Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.
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Affiliation(s)
- Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
| | - Steven A Miller
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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Trotter AJ, Aydin A, Strinden MJ, O'Grady J. Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance. Curr Opin Microbiol 2019; 51:39-45. [PMID: 31077935 DOI: 10.1016/j.mib.2019.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/04/2019] [Accepted: 03/08/2019] [Indexed: 10/26/2022]
Abstract
The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 2050 unless steps are taken to prevent this looming crisis. Microbiological culture is the gold standard for the diagnosis of bacterial/fungal pathogens and antimicrobial resistance and takes 48 hours or longer. Hence, antibiotic prescriptions are rarely based on a definitive diagnosis and patients often receive inappropriate treatment. Rapid diagnostic tools are urgently required to guide appropriate antimicrobial therapy, thereby improving patient outcomes and slowing AMR development. We discuss new technologies for rapid infection diagnosis including: sample-in-answer-out PCR-based tests, BioFire FilmArray and Curetis Unyvero; rapid susceptibility tests, Accelerate Pheno and microfluidic tests; and sequencing-based approaches, focusing on targeted and clinical metagenomic nanopore sequencing.
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Affiliation(s)
- Alexander J Trotter
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Alp Aydin
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Michael J Strinden
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Justin O'Grady
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
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67
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Miller S, Naccache SN, Samayoa E, Messacar K, Arevalo S, Federman S, Stryke D, Pham E, Fung B, Bolosky WJ, Ingebrigtsen D, Lorizio W, Paff SM, Leake JA, Pesano R, DeBiasi R, Dominguez S, Chiu CY. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res 2019; 29:831-842. [PMID: 30992304 PMCID: PMC6499319 DOI: 10.1101/gr.238170.118] [Citation(s) in RCA: 310] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we developed and validated a clinical mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, generate an automated summary of detected pathogens, and provide a graphical user interface for evaluating and interpreting results. We established quality metrics, threshold values, and limits of detection of 0.2-313 genomic copies or colony forming units per milliliter for each representative organism type. Gross hemolysis and excess host nucleic acid reduced assay sensitivity; however, spiked phages used as internal controls were reliable indicators of sensitivity loss. Diagnostic test accuracy was evaluated by blinded mNGS testing of 95 patient samples, revealing 73% sensitivity and 99% specificity compared to original clinical test results, and 81% positive percent agreement and 99% negative percent agreement after discrepancy analysis. Subsequent mNGS challenge testing of 20 positive CSF samples prospectively collected from a cohort of pediatric patients hospitalized with meningitis, encephalitis, and/or myelitis showed 92% sensitivity and 96% specificity relative to conventional microbiological testing of CSF in identifying the causative pathogen. These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.
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Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California 90027, USA
| | - Erik Samayoa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kevin Messacar
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Elizabeth Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Becky Fung
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | | | - Danielle Ingebrigtsen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Walter Lorizio
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Sandra M Paff
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - John A Leake
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92675, USA
| | - Rick Pesano
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92675, USA
| | - Roberta DeBiasi
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC 20010, USA
- Department of Pediatrics, Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine, Washington, DC 20037, USA
| | - Samuel Dominguez
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, California 94143, USA
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Peker N, Garcia-Croes S, Dijkhuizen B, Wiersma HH, van Zanten E, Wisselink G, Friedrich AW, Kooistra-Smid M, Sinha B, Rossen JWA, Couto N. A Comparison of Three Different Bioinformatics Analyses of the 16S-23S rRNA Encoding Region for Bacterial Identification. Front Microbiol 2019; 10:620. [PMID: 31040829 PMCID: PMC6476902 DOI: 10.3389/fmicb.2019.00620] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/12/2019] [Indexed: 11/25/2022] Open
Abstract
Rapid and reliable identification of bacterial pathogens directly from patient samples is required for optimizing antimicrobial therapy. Although Sanger sequencing of the 16S ribosomal RNA (rRNA) gene is used as a molecular method, species identification and discrimination is not always achievable for bacteria as their 16S rRNA genes have sometimes high sequence homology. Recently, next generation sequencing (NGS) of the 16S–23S rRNA encoding region has been proposed for reliable identification of pathogens directly from patient samples. However, data analysis is laborious and time-consuming and a database for the complete 16S–23S rRNA encoding region is not available. Therefore, a better, faster, and stronger approach is needed for NGS data analysis of the 16S–23S rRNA encoding region. We compared speed and diagnostic accuracy of different data analysis approaches: de novo assembly followed by Basic Local Alignment Search Tool (BLAST), operational taxonomic unit (OTU) clustering, or mapping using an in-house developed 16S–23S rRNA encoding region database for the identification of bacterial species. De novo assembly followed by BLAST using the in-house database was superior to the other methods, resulting in the shortest turnaround time (2 h and 5 min), approximately 2 h less than OTU clustering and 4.5 h less than mapping, and a sensitivity of 80%. Mapping was the slowest and most laborious data analysis approach with a sensitivity of 60%, whereas OTU clustering was the least laborious approach with 70% sensitivity. Although the in-house database requires more sequence entries to improve the sensitivity, the combination of de novo assembly and BLAST currently appears to be the optimal approach for data analysis.
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Affiliation(s)
- Nilay Peker
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sharron Garcia-Croes
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Brigitte Dijkhuizen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Henry H Wiersma
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Evert van Zanten
- Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - Guido Wisselink
- Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Mirjam Kooistra-Smid
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - Bhanu Sinha
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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69
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Liu H, Guo M, Jiang Y, Cao Y, Qian Q, He X, Huang K, Zhang J, Xu W. Diagnosing and tracing the pathogens of infantile infectious diarrhea by amplicon sequencing. Gut Pathog 2019; 11:12. [PMID: 30992716 PMCID: PMC6451272 DOI: 10.1186/s13099-019-0292-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/19/2019] [Indexed: 01/14/2023] Open
Abstract
Background Metagenomic methods have been widely applied to study the relationship between gut microbiota and human health. To test whether metagenomic amplicon sequencing could be an effective method to diagnose and trace the pathogens of infantile infectious diarrhea, the fecal samples of 20 diarrheic and 13 healthy infants were collected. After 16S rDNA amplicon sequencing, diversity analyses were carried out. The relationship between the pathogens of the gut microbiota and geography of patients was analyzed. Results The diversity of the gut microbiota in diarrheic infants was significantly lower than that of the gut microbiota in healthy ones and that, the composition of gut microbiota in the diarrheic group was significantly different than that of the gut microbiota in the healthy group. The results also indicated that in some of the patients, the amounts of Escherichia coli were significantly increased in the diarrheic infants, which was in agreement with the result of the qPCR analysis. Using a geographical map, we found some patterns between pathogen source and geographical location. This is helpful for an early warning of the disease. Conclusions The method of using high-throughput DNA sequencing and a comprehensive and deep data analysis can be a new strategy to detect and trace pathogens in infantile infectious diarrhea. Trial registration Diagnosing and tracing the pathogens of infantile infectious diarrhea by amplicon sequencing, ChiCTR-DDD-1701088, Registered 16 March 2017-Retrospectively registered, http://www.chictr.org.cn/showproj.aspx?proj=18477
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Affiliation(s)
- Haiyan Liu
- 1School of Public Health, North China University of Science and Technology, Tangshan, Hebei China
| | - Mingzhang Guo
- 2Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yuanchunzi Jiang
- 2Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yanhua Cao
- 1School of Public Health, North China University of Science and Technology, Tangshan, Hebei China
| | - Qingzeng Qian
- 1School of Public Health, North China University of Science and Technology, Tangshan, Hebei China
| | - Xiaoyun He
- 2Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, China
| | - Kunlun Huang
- 2Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jianwei Zhang
- 3Physical Education Department, Tangshan Normal University, Tangshan, Hebei China
| | - Wentao Xu
- 2Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, China.,4Laboratory of Food Safety and Molecular Biology, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Haidian District, Beijing, 100083 China
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70
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Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory. Eur J Clin Microbiol Infect Dis 2019; 38:1059-1070. [PMID: 30834996 PMCID: PMC6520317 DOI: 10.1007/s10096-019-03520-3] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022]
Abstract
Recent advancements in next-generation sequencing (NGS) have provided the foundation for modern studies into the composition of microbial communities. The use of these NGS methods allows for the detection and identification of (‘difficult-to-culture’) microorganisms using a culture-independent strategy. In the field of routine clinical diagnostics however, the application of NGS is currently limited to microbial strain typing for epidemiological purposes only, even though the implementation of NGS for microbial community analysis may yield clinically important information. This lack of NGS implementation is due to many different factors, including issues relating to NGS method standardization and result reproducibility. In this review article, the authors provide a general introduction to the most widely used NGS methods currently available (i.e., targeted amplicon sequencing and shotgun metagenomics) and the strengths and weaknesses of each method is discussed. The focus of the publication then shifts toward 16S rRNA gene NGS methods, which are currently the most cost-effective and widely used NGS methods for research purposes, and are therefore more likely to be successfully implemented into routine clinical diagnostics in the short term. In this respect, the experimental pitfalls and biases created at each step of the 16S rRNA gene NGS workflow are explained, as well as their potential solutions. Finally, a novel diagnostic microbiota profiling platform (‘MYcrobiota’) is introduced, which was developed by the authors by taking into consideration the pitfalls, biases, and solutions explained in this article. The development of the MYcrobiota, and future NGS methodologies, will help pave the way toward the successful implementation of NGS methodologies into routine clinical diagnostics.
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71
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Zahedi A, Gofton AW, Greay T, Monis P, Oskam C, Ball A, Bath A, Watkinson A, Robertson I, Ryan U. Profiling the diversity of Cryptosporidium species and genotypes in wastewater treatment plants in Australia using next generation sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:635-648. [PMID: 30743878 DOI: 10.1016/j.scitotenv.2018.07.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 06/09/2023]
Abstract
Wastewater recycling is an increasingly popular option in worldwide to reduce pressure on water supplies due to population growth and climate change. Cryptosporidium spp. are among the most common parasites found in wastewater and understanding the prevalence of human-infectious species is essential for accurate quantitative microbial risk assessment (QMRA) and cost-effective management of wastewater. The present study conducted next generation sequencing (NGS) to determine the prevalence and diversity of Cryptosporidium species in 730 raw influent samples from 25 Australian wastewater treatment plants (WWTPs) across three states: New South Wales (NSW), Queensland (QLD) and Western Australia (WA), between 2014 and 2015. All samples were screened for the presence of Cryptosporidium at the 18S rRNA (18S) locus using quantitative PCR (qPCR), oocyst numbers were determined directly from the qPCR data using DNA standards calibrated by droplet digital PCR, and positives were characterized using NGS of 18S amplicons. Positives were also screened using C. parvum and C. hominis specific qPCRs. The overall Cryptosporidium prevalence was 11.4% (83/730): 14.3% (3/21) in NSW; 10.8% (51/470) in QLD; and 12.1% (29/239) in WA. A total of 17 Cryptosporidium species and six genotypes were detected by NGS. In NSW, C. hominis and Cryptosporidium rat genotype III were the most prevalent species (9.5% each). In QLD, C. galli, C. muris and C. parvum were the three most prevalent species (7.7%, 5.7%, and 4.5%, respectively), while in WA, C. meleagridis was the most prevalent species (6.3%). The oocyst load/Litre ranged from 70 to 18,055 oocysts/L (overall mean of 3426 oocysts/L: 4746 oocysts/L in NSW; 3578 oocysts/L in QLD; and 3292 oocysts/L in WA). NGS-based profiling demonstrated that Cryptosporidium is prevalent in the raw influent across Australia and revealed a large diversity of Cryptosporidium species and genotypes, which indicates the potential contribution of livestock, wildlife and birds to wastewater contamination.
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Affiliation(s)
- Alireza Zahedi
- School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
| | - Alexander W Gofton
- School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
| | - Telleasha Greay
- School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
| | - Paul Monis
- Australian Water Quality Centre, South Australian Water Corporation, Adelaide, Australia
| | - Charlotte Oskam
- School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
| | | | | | - Andrew Watkinson
- Seqwater, Ipswich, Queensland, Australia; University of Queensland, St Lucia, Queensland, Australia
| | - Ian Robertson
- School of Veterinary and Life Sciences, Murdoch University, Perth, Australia; China-Australia Joint Research and Training Centre for Veterinary Epidemiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Una Ryan
- School of Veterinary and Life Sciences, Murdoch University, Perth, Australia.
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72
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Gu W, Miller S, Chiu CY. Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018; 14:319-338. [PMID: 30355154 DOI: 10.1146/annurev-pathmechdis-012418-012751] [Citation(s) in RCA: 678] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its advent in 2004, and it has emerged as an enabling technological platform for the detection and taxonomic characterization of microorganisms in clinical samples from patients. This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations. The review covers ( a) next-generation sequencing technologies and common platforms, ( b) next-generation sequencing assay workflows in the clinical microbiology laboratory, ( c) bioinformatics analysis of metagenomic next-generation sequencing data, ( d) validation and use of metagenomic next-generation sequencing for diagnosing infectious diseases, and ( e) significant case reports and studies in this area. Next-generation sequencing is a new technology that has the promise to enhance our ability to diagnose, interrogate, and track infectious diseases.
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Affiliation(s)
- Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA; .,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California 94107, USA
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73
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Minogue TD, Koehler JW, Stefan CP, Conrad TA. Next-Generation Sequencing for Biodefense: Biothreat Detection, Forensics, and the Clinic. Clin Chem 2018; 65:383-392. [PMID: 30352865 DOI: 10.1373/clinchem.2016.266536] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/22/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) is revolutionizing a variety of molecular biology fields including bioforensics, biosurveillance, and infectious disease diagnostics. For pathogen detection, the ability to sequence all nucleic acids in a sample allows near limitless multiplexability, free from a priori knowledge regarding an etiologic agent as is typically required for targeted molecular assays such as real-time PCR. Furthermore, sequencing capabilities can generate in depth genomic information, allowing detailed molecular epidemiological studies and bioforensics analysis, which is critical for source agent identification in a biothreat outbreak. However, lack of analytical specificity, inherent to NGS, presents challenges for regulated applications such as clinical diagnostics and molecular attribution. CONTENT Here, we discuss NGS applications in the context of preparedness and biothreat readiness. Specifically, we investigate current and future applications of NGS technologies to affect the fields of biosurveillance, bioforensics, and clinical diagnostics with specific focus on biodefense. SUMMARY Overall, there are many advantages to the implementation of NGS for preparedness and readiness against biowarfare agents, from forensics to diagnostics. However, appropriate caveats must be associated with any technology. This includes NGS. While NGS is not the panacea replacing all molecular techniques, it will greatly enhance the ability to detect, characterize, and diagnose biowarfare agents, thus providing an excellent addition to the biodefense toolbox of biosurveillance, bioforensics, and biothreat diagnosis.
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Affiliation(s)
- Timothy D Minogue
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD.
| | - Jeffrey W Koehler
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
| | - Christopher P Stefan
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
| | - Turner A Conrad
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD
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74
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Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018; 4:116-126. [PMID: 30263975 DOI: 10.1016/j.cobme.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is one of the biggest threats to public health. The rapid emergence of resistant bacterial pathogens endangers the efficacy of current antibiotics and has led to increasing mortality and economic burden. This crisis calls for more rapid and accurate diagnosis to detect and identify pathogens, as well as to characterize their response to antibiotics. Building on this foundation, treatment options also need to be improved to use current antibiotics more effectively and develop alternative strategies that complement the use of antibiotics. We here review recent developments in diagnosis and treatment of bacterial pathogens with a focus on quantitative biology and synthetic biology approaches.
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Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Jonathan H Bethke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA
| | - Meidi Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, 27708, USA
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75
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Wan XL, McLaughlin RW, Zheng JS, Hao YJ, Fan F, Tian RM, Wang D. Microbial communities in different regions of the gastrointestinal tract in East Asian finless porpoises (Neophocaena asiaeorientalis sunameri). Sci Rep 2018; 8:14142. [PMID: 30237562 PMCID: PMC6147976 DOI: 10.1038/s41598-018-32512-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 08/13/2018] [Indexed: 01/26/2023] Open
Abstract
Mammalian gastrointestinal (GI) tract microbial communities are critical for host health. However, the microbiota along the GI tract in cetaceans has not been well characterized compared to other animals. In this study, the bacteria and fungi present in the stomach, foregut, hindgut and feces, of East Asian finless porpoises (Neophocaena asiaeorientalis sunameri, EAFPs) were characterized using high-throughput sequencing analysis. The bacterial and fungal diversity and richness in the stomach, hindgut and fecal samples tended to be higher than those in the foregut. Bacterial taxonomic compositions found in the hindgut and feces were different from those seen in the stomach and foregut. A greater proportion of strict anaerobic bacteria including Clostridia, Fusobacteria, and Ruminococcaceae were found in the hindgut and fecal samples. The fungal communities present in stomach samples differed from those detected in other regions to some extent. Zygomycota and Neocallimastigomycota were more predominant in the stomach. Some potential pathogens, such as Helicobacter spp. and Vibrio spp., were commonly present along the GI tract. Our study confirms that the fecal microbiota can represent the whole GI tract to some extent because of their relatively higher microbial diversity and presence of potential pathogens. Our study provides the first comprehensive characterization of the EAFPs GI microbiota, expanding on the current knowledge about the bacterial diversity in the GI tract of cetaceans. In addition, this is the first study characterizing the fungal diversity of any species of porpoise.
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Affiliation(s)
- Xiao-Ling Wan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Richard William McLaughlin
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,General Studies, Gateway Technical College, Kenosha, WI, 53144, USA
| | - Jin-Song Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Yu-Jiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fei Fan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ren-Mao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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76
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Vargas-Albores F, Martínez-Córdova LR, Martínez-Porchas M, Calderón K, Lago-Lestón A. Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences. Biotechnol Genet Eng Rev 2018; 35:69-91. [PMID: 30221593 DOI: 10.1080/02648725.2018.1513230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.
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Affiliation(s)
- Francisco Vargas-Albores
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Luis R Martínez-Córdova
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
| | - Marcel Martínez-Porchas
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Kadiya Calderón
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
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77
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Grahl N, Dolben EL, Filkins LM, Crocker AW, Willger SD, Morrison HG, Sogin ML, Ashare A, Gifford AH, Jacobs NJ, Schwartzman JD, Hogan DA. Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA. mSphere 2018; 3:e00292-18. [PMID: 30089648 PMCID: PMC6083091 DOI: 10.1128/msphere.00292-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/10/2018] [Indexed: 12/26/2022] Open
Abstract
Here, we report an approach to detect diverse bacterial and fungal taxa in complex samples by direct analysis of community RNA in one step using NanoString probe sets. We designed rRNA-targeting probe sets to detect 42 bacterial and fungal genera or species common in cystic fibrosis (CF) sputum and demonstrated the taxon specificity of these probes, as well as a linear response over more than 3 logs of input RNA. Culture-based analyses correlated qualitatively with relative abundance data on bacterial and fungal taxa obtained by NanoString, and the analysis of serial samples demonstrated the use of this method to simultaneously detect bacteria and fungi and to detect microbes at low abundance without an amplification step. Compared at the genus level, the relative abundances of bacterial taxa detected by analysis of RNA correlated with the relative abundances of the same taxa as measured by sequencing of the V4V5 region of the 16S rRNA gene amplified from community DNA from the same sample. We propose that this method may complement other methods designed to understand dynamic microbial communities, may provide information on bacteria and fungi in the same sample with a single assay, and with further development, may provide quick and easily interpreted diagnostic information on diverse bacteria and fungi at the genus or species level.IMPORTANCE Here we demonstrate the use of an RNA-based analysis of specific taxa of interest, including bacteria and fungi, within microbial communities. This multiplex method may be useful as a means to identify samples with specific combinations of taxa and to gain information on how specific populations vary over time and space or in response to perturbation. A rapid means to measure bacterial and fungal populations may aid in the study of host response to changes in microbial communities.
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Affiliation(s)
- Nora Grahl
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Emily L Dolben
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Laura M Filkins
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Alex W Crocker
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Sven D Willger
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Mitchell L Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Alix Ashare
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Alex H Gifford
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Nicholas J Jacobs
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Joseph D Schwartzman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Deborah A Hogan
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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78
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SEO BJ, SONG ET, LEE K, KIM JW, JEONG CG, MOON SH, SON JS, KANG SH, CHO HS, JUNG BY, KIM WI. Evaluation of the broad-spectrum lytic capability of bacteriophage cocktails against various Salmonella serovars and their effects on weaned pigs infected with Salmonella Typhimurium. J Vet Med Sci 2018; 80:851-860. [PMID: 29618667 PMCID: PMC6021886 DOI: 10.1292/jvms.17-0501] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/19/2018] [Indexed: 11/22/2022] Open
Abstract
The broad-spectrum lytic capability of Salmonella bacteriophages against various Salmonella species was evaluated to determine their potential as an alternative for antibiotics, and the safety and preventive effects of the bacteriophages were assessed on mice and pigs. Four bacteriophage cocktails were prepared using 13 bacteriophages, and the lytic capability of the four bacteriophage cocktails was tested using Salmonella reference strains and field isolates. Bacteriophage cocktail C (SEP-1, SGP-1, STP-1, SS3eP-1, STP-2, SChP-1, SAP-1, SAP-2; ≥109 pfu/ml) showed the best lytic activity against the Salmonella reference strains (100% of 34) and field isolates (92.5% of 107). Fifty mice were then orally inoculated with bacteriophage cocktail C to determine the distribution of bacteriophages in various organs, blood and feces. The effects of bacteriophages on Salmonella infection in weaned pigs (n=15) were also evaluated through an experimental challenge with Salmonella Typhimurium after treatment with bacteriophage cocktail C. All mice exhibited distribution of the bacteriophages in all organs, blood and feces until 15 days post infection (dpi). After 35 dpi, bacteriophages were not detected in any of these specimens. As demonstrated in a pig challenge study, treatment with bacteriophage cocktail C reduced the level of Salmonella shedding in feces. The metagenomic analyses of these pig feces also revealed that bacteriophage treatment decreased the number of species of the Enterobacteriaceae family without significant disturbance to the normal fecal flora. This study showed that bacteriophages effectively controlled Salmonella in a pig challenge model and could be a good alternative for antibiotics to control Salmonella infection.
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Affiliation(s)
- Byoung-Joo SEO
- College of Veterinary Medicine, Chonbuk National University,
Iksan 54596, Republic of Korea
| | - Eu-Tteum SONG
- Bacterial Disease Division, Animal and Plant Quarantine
Agency, Gimcheon 39660, Republic of Korea
| | - Kichan LEE
- Bacterial Disease Division, Animal and Plant Quarantine
Agency, Gimcheon 39660, Republic of Korea
| | - Jong-Won KIM
- College of Veterinary Medicine, Chonbuk National University,
Iksan 54596, Republic of Korea
| | - Chang-Gi JEONG
- College of Veterinary Medicine, Chonbuk National University,
Iksan 54596, Republic of Korea
| | - Sung-Hyun MOON
- College of Veterinary Medicine, Chonbuk National University,
Iksan 54596, Republic of Korea
| | - Jee Soo SON
- iNtRON Biotechnology, Inc., Room 903, JungAng Induspia V,
137, Sagimakgol-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, 13202, Republic of Korea
| | - Sang Hyeon KANG
- iNtRON Biotechnology, Inc., Room 903, JungAng Induspia V,
137, Sagimakgol-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, 13202, Republic of Korea
| | - Ho-Seong CHO
- College of Veterinary Medicine, Chonbuk National University,
Iksan 54596, Republic of Korea
| | - Byeong Yeal JUNG
- Bacterial Disease Division, Animal and Plant Quarantine
Agency, Gimcheon 39660, Republic of Korea
| | - Won-Il KIM
- College of Veterinary Medicine, Chonbuk National University,
Iksan 54596, Republic of Korea
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79
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Rocchetti TT, Silbert S, Gostnell A, Kubasek C, Jerris R, Vong J, Widen R. Rapid detection of four non-fermenting Gram-negative bacteria directly from cystic fibrosis patient's respiratory samples on the BD MAX™ system. Pract Lab Med 2018; 12:e00102. [PMID: 30009245 PMCID: PMC6041425 DOI: 10.1016/j.plabm.2018.e00102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/13/2018] [Accepted: 05/23/2018] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to develop a multiplex PCR test to detect Achromobacter xylosoxidans (AX), Burkholderia cepacia (BC), Pseudomonas aeruginosa (PSA) and Stenotrophomonas maltophilia (SM) directly from CF patient's respiratory samples using the open mode of the BD MAX™ System. A total of 402 CF respiratory samples were evaluated by culture and PCR. Specific sets of primers and probes for each target were designed in-house. Out of 402 samples tested, 196 were identified as negative and 206 as positive by culture for AX, PSA, BC and SM. Among culture positive samples, PCR detected 21/27 AX, 4/5 BC, 138/140 PSA and 29/34 SM. In addition, PCR assay identified 35 samples as positive that were initially negative by culture for those 4 targets. The CF BDM test proved to be an excellent tool to detect AX, BC, PSA and SM by real-time PCR on an automated platform.
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Affiliation(s)
- Talita T. Rocchetti
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
- Laboratório Especial de Microbiologia Clínica (LEMC), Federal University of São Paulo/UNIFESP, São Paulo, SP, Brazil
| | - Suzane Silbert
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
- Correspondence to: Esoteric Testing Laboratory, Tampa General Hospital, 1 Tampa General Circle, Tampa, FL 33606-3571, USA.
| | - Alicia Gostnell
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
| | - Carly Kubasek
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
| | | | | | - Raymond Widen
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
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80
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Tsuchiya Y, Loza E, Villa-Gomez G, Trujillo CC, Baez S, Asai T, Ikoma T, Endoh K, Nakamura K. Metagenomics of Microbial Communities in Gallbladder Bile from Patients with Gallbladder Cancer or Cholelithiasis. Asian Pac J Cancer Prev 2018; 19:961-967. [PMID: 29693356 PMCID: PMC6031792 DOI: 10.22034/apjcp.2018.19.4.961] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Salmonella typhi and Helicobacter infections have been shown to increase risk of gallbladder cancer (GBC), but findings have been inconsistent. Other bacterial infections may also be associated with GBC. However, information on microbial pathogens in gallbladder bile of GBC patients is scarce. We aimed to investigate the microbial communities in gallbladder bile of patients with GBC and cholelithiasis (CL). Seven GBC patients and 30 CL patients were enrolled in this study. Genomic DNA was extracted from bile and the V3-V4 region of 16S rRNA was amplified. The sequencing results were compared with the 16S database, and the bacteria were identified by homology searches and phylogenetic analysis. DNA was detected in the bile of three GBC (42.9%; Bolivia, 1; Chile, 2) and four CL patients (13.3%; Bolivia, 1; Chile, 3). Of the 37 patients, 30 (81.1%) were negative and unable to analyze. Salmonella typhi and Helicobacter sp. were not detected in bile from any GBC patients. As the predominant species, Fusobacterium nucleatum, Escherichia coli, and Enetrobacter sp. were detected in bile from GBC patients. Those in bile from CL patients were Escherichia coli, Salmonella sp., and Enerococcus gallinarum. Escherichia coli was detected in bile samples from both GBC and CL patients. Whether the bacteria detected in bile from GBC patients would associated with the development of GBC warrant further investigation.
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Affiliation(s)
- Yasuo Tsuchiya
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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81
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Di Segni A, Braun T, BenShoshan M, Farage Barhom S, Glick Saar E, Cesarkas K, Squires JE, Keller N, Haberman Y. Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing. J Vis Exp 2018. [PMID: 29608151 DOI: 10.3791/56845] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The human intestinal microbiome plays a central role in protecting cells from injury, in processing energy and nutrients, and in promoting immunity. Deviations from what is considered a healthy microbiota composition (dysbiosis) may impair vital functions leading to pathologic conditions. Recent and ongoing research efforts have been directed toward the characterization of associations between microbial composition and human health and disease. Advances in high-throughput sequencing technologies enable characterization of the gut microbial composition. These methods include 16S rRNA-amplicon sequencing and shotgun sequencing. 16S rRNA-amplicon sequencing is used to profile taxonomical composition, while shotgun sequencing provides additional information about gene predictions and functional annotation. An advantage in using a targeted sequencing method of the 16S rRNA gene variable region is its substantially lower cost compared to shotgun sequencing. Sequence differences in the 16S rRNA gene are used as a microbial fingerprint to identify and quantify different taxa within an individual sample. Major international efforts have enlisted standards for 16S rRNA-amplicon sequencing. However, several studies report a common source of variation caused by batch effect. To minimize this effect, uniformed protocols for sample collection, processing, and sequencing must be implemented. This protocol proposes the integration of broadly used protocols starting from fecal sample collection to data analyses. This protocol includes a column-free, direct-PCR approach that enables simultaneous handling and DNA extraction of large numbers of fecal samples, along with PCR amplification of the V4 region. In addition, the protocol describes the analysis pipeline and provides a script using the latest version of QIIME (QIIME 2 version 2017.7.0 and DADA2). This step-by-step protocol is aimed to guide those interested in initiating the use of 16S rRNA-amplicon sequencing in a robust, reproductive, easy to use, detailed way.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yael Haberman
- Sheba Medical Center; Cincinnati Children's Hospital Medical Center;
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82
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Boers SA, Hiltemann SD, Stubbs AP, Jansen R, Hays JP. Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics. Eur J Clin Microbiol Infect Dis 2018; 37:1081-1089. [PMID: 29549470 PMCID: PMC5948305 DOI: 10.1007/s10096-018-3220-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 12/19/2022]
Abstract
Microbiota profiling has the potential to greatly impact on routine clinical diagnostics by detecting DNA derived from live, fastidious, and dead bacterial cells present within clinical samples. Such results could potentially be used to benefit patients by influencing antibiotic prescribing practices or to generate new classical-based diagnostic methods, e.g., culture or PCR. However, technical flaws in 16S rRNA gene next-generation sequencing (NGS) protocols, together with the requirement for access to bioinformatics, currently hinder the introduction of microbiota analysis into clinical diagnostics. Here, we report on the development and evaluation of an “end-to-end” microbiota profiling platform (MYcrobiota), which combines our previously validated micelle PCR/NGS (micPCR/NGS) methodology with an easy-to-use, dedicated bioinformatics pipeline. The newly designed bioinformatics pipeline processes micPCR/NGS data automatically and summarizes the results in interactive, but simple web reports. In order to explore the utility of MYcrobiota in clinical diagnostics, 47 clinical samples (40 “damaged skin” samples and 7 synovial fluids) were investigated using routine bacterial culture as comparator. MYcrobiota confirmed the presence of bacterial DNA in 37/37 culture-positive samples and detected bacterial taxa in 2/10 culture-negative samples. Moreover, 36/38 potentially relevant aerobic bacterial taxa and 3/3 mixtures of anaerobic bacteria were identified using culture and MYcrobiota, with the sensitivity and specificity being 95%. Interestingly, the majority of the 448 bacterial taxa identified using MYcrobiota were not identified using culture, which could potentially have an impact on clinical decision-making. Taken together, the development of MYcrobiota is a promising step towards the introduction of microbiota analysis into clinical diagnostic laboratories.
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Affiliation(s)
- Stefan A Boers
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre Rotterdam (Erasmus MC), Wytemaweg 80, 3015 CN, Rotterdam, the Netherlands
| | - Saskia D Hiltemann
- Department of Bioinformatics, Erasmus University Medical Centre Rotterdam (Erasmus MC), Rotterdam, the Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus University Medical Centre Rotterdam (Erasmus MC), Rotterdam, the Netherlands
| | - Ruud Jansen
- Department of Molecular Biology, Regional Laboratory of Public Health Kennemerland, Haarlem, the Netherlands
| | - John P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre Rotterdam (Erasmus MC), Wytemaweg 80, 3015 CN, Rotterdam, the Netherlands.
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83
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Kim SL, Gordon SM, Shrestha NK. Distribution of streptococcal groups causing infective endocarditis: a descriptive study. Diagn Microbiol Infect Dis 2018; 91:269-272. [PMID: 29567126 DOI: 10.1016/j.diagmicrobio.2018.02.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/12/2018] [Accepted: 02/21/2018] [Indexed: 11/17/2022]
Abstract
The purpose of this study was to describe the distribution of streptococci causing infective endocarditis (IE). A total of 296 patients with definite IE admitted from July 2007 to December 2014 were identified, with microbial identification done by a combination of blood culture, valve culture, and valve polymerase chain reaction (PCR). The overall distribution of streptococci was 76% viridans (n = 224), 17% pyogenic (50), 6% nutritionally variant (17), and 2% anaerobic (5). Sixty-three (21%) viridans group streptococci were not identified further. The distribution of the remaining 161 viridans group streptococci was Streptococcus mitis group 61%, S. bovis group 15%, S. mutans group 13%, S. anginosus group 9%, and S. salivarius group 1%. Of the 50 pyogenic streptococci, 78% were S. agalactiae and 16% were S. dysgalactiae. PCR was significantly more sensitive than culture in identifying streptococci in excised heart valves.
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Affiliation(s)
- So Lim Kim
- Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106, USA.
| | - Steven M Gordon
- Department of Infectious Diseases, Cleveland Clinic, 9500 Euclid Avenue, G21, Cleveland, OH 44195, USA.
| | - Nabin K Shrestha
- Department of Infectious Diseases, Cleveland Clinic, 9500 Euclid Avenue, G21, Cleveland, OH 44195, USA.
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84
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Banerjee S, Sar A, Misra A, Pal S, Chakraborty A, Dam B. Increased productivity in poultry birds by sub-lethal dose of antibiotics is arbitrated by selective enrichment of gut microbiota, particularly short-chain fatty acid producers. Microbiology (Reading) 2018; 164:142-153. [PMID: 29393019 DOI: 10.1099/mic.0.000597] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Sohini Banerjee
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
- Department of Environmental Studies, Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Abhijit Sar
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Arijit Misra
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Srikanta Pal
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Arindom Chakraborty
- Department of Statistics, Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
| | - Bomba Dam
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235, India
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85
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Detection of 16S rRNA and KPC Genes from Complex Matrix Utilizing a Molecular Inversion Probe Assay for Next-Generation Sequencing. Sci Rep 2018; 8:2028. [PMID: 29391471 PMCID: PMC5794912 DOI: 10.1038/s41598-018-19501-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/27/2017] [Indexed: 11/08/2022] Open
Abstract
Targeted sequencing promises to bring next-generation sequencing (NGS) into routine clinical use for infectious disease diagnostics. In this context, upfront processing techniques, including pathogen signature enrichment, must amplify multiple targets of interest for NGS to be relevant when applied to patient samples with limited volumes. Here, we demonstrate an optimized molecular inversion probe (MIP) assay targeting multiple variable regions within the 16S ribosomal gene for the identification of biothreat and ESKAPE pathogens in a process that significantly reduces complexity, labor, and processing time. Probes targeting the Klebsiella pneumoniae carbapenemase (KPC) antibiotic resistance (AR) gene were also included to demonstrate the ability to concurrently identify etiologic agent and ascertain valuable secondary genetic information. Our assay captured gene sequences in 100% of mock clinical samples prepared from flagged positive blood culture bottles. Using a simplified processing and adjudication method for mapped sequencing reads, genus and species level concordance was 100% and 80%, respectively. In addition, sensitivity and specificity for KPC gene detection was 100%. Our MIP assay produced sequenceable amplicons for the identification of etiologic agents and the detection of AR genes directly from blood culture bottles in a simplified single tube assay.
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86
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Kozlov A, Bean L, Hill EV, Zhao L, Li E, Wang GP. Molecular Identification of Bacteria in Intra-abdominal Abscesses Using Deep Sequencing. Open Forum Infect Dis 2018; 5:ofy025. [PMID: 29479554 DOI: 10.1093/ofid/ofy025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/20/2018] [Indexed: 11/14/2022] Open
Abstract
Background Intra-abdominal abscesses are localized collections of pus, which generally arise from a breach in the normal mucosal defense barrier that allows bacteria from gastrointestinal tract, and less commonly from the gynecologic or urinary tract, to induce inflammation, resulting in an infection. The microbiology of these abscesses is usually polymicrobial, associated with the primary disease process. However, the microbial identity, diversity and richness in intra-abdominal abscesses have not been well characterized, due in part to the difficulty in cultivating commensal organisms using standard culture-based techniques. Methods We used culture-independent 16S rRNA Illumina sequencing to characterize bacterial communities in intra-abdominal abscesses collected by percutaneous drainage. A total of 43 abscess samples, including 19 (44.2%) Gram stain and culture-negative specimens, were analyzed and compared with results from conventional microbiologic cultures. Results Microbial composition was determined in 8 of 19 culture-negative samples and 18 of 24 culture-positive samples, identifying a total of 221 bacterial taxa or operational taxonomic units (OTUs) and averaging 13.1 OTUs per sample (interquartile range, 8-16.5 OTUs). Microbial richness for monomicrobial and polymicrobial samples was significantly higher than culture-negative samples (17 and 15.2 OTUs vs 8 OTUs, respectively), with a trend toward a higher microbial diversity (Shannon diversity index of 0.87 and 1.18 vs 0.58, respectively). Conclusions The bacterial consortia identified by cultures correlated poorly with the microbial composition determined by 16S rRNA sequencing, and in most cases, the cultured isolates were minority constituents of the overall abscess microbiome. Intra-abdominal abscesses were generally polymicrobial with a surprisingly high microbial diversity, but standard culture-based techniques failed to reveal this diversity. These data suggest that molecular-based approaches may be helpful for documenting the presence of bacteria in intra-abdominal abscesses where standard cultures are unrevealing, particularly in the setting of prior antibiotic exposure.
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Affiliation(s)
- Andrew Kozlov
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Lorenzo Bean
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Emilie V Hill
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
- Infectious Diseases Section, Medical Service, North Florida/South Georgia Veterans Health System, Gainesville, Florida
| | - Lisa Zhao
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Eric Li
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Gary P Wang
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
- Infectious Diseases Section, Medical Service, North Florida/South Georgia Veterans Health System, Gainesville, Florida
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87
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Cystic Fibrosis Airway Microbiome: Overturning the Old, Opening the Way for the New. J Bacteriol 2018; 200:JB.00561-17. [PMID: 29084859 DOI: 10.1128/jb.00561-17] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The genetic disease cystic fibrosis (CF) is associated with chronic airway infections that are a proximal cause of death in many patients with this affliction. Classic microbiology studies focusing on canonical pathogens resulted in the development of a common set of views regarding the nature of the airway infections associated with this disease, and these ideas have influenced everything from the way infections are treated to how clinical trials for new CF-targeted antibiotics are designed and the focus of CF-related research topics. Recent culture-independent studies have prompted us to rethink, and in some cases discard, some of these long-held views. In this piece, I argue that an updated view of the complicated chronic infections associated with CF, thanks in large part to culture-independent studies of sputum and bronchoalveolar lavage fluid samples, should be leveraged to develop new strategies to treat these recalcitrant infections.
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88
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Greay TL, Gofton AW, Paparini A, Ryan UM, Oskam CL, Irwin PJ. Recent insights into the tick microbiome gained through next-generation sequencing. Parasit Vectors 2018; 11:12. [PMID: 29301588 PMCID: PMC5755153 DOI: 10.1186/s13071-017-2550-5] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023] Open
Abstract
The tick microbiome comprises communities of microorganisms, including viruses, bacteria and eukaryotes, and is being elucidated through modern molecular techniques. The advent of next-generation sequencing (NGS) technologies has enabled the genes and genomes within these microbial communities to be explored in a rapid and cost-effective manner. The advantages of using NGS to investigate microbiomes surpass the traditional non-molecular methods that are limited in their sensitivity, and conventional molecular approaches that are limited in their scalability. In recent years the number of studies using NGS to investigate the microbial diversity and composition of ticks has expanded. Here, we provide a review of NGS strategies for tick microbiome studies and discuss the recent findings from tick NGS investigations, including the bacterial diversity and composition, influential factors, and implications of the tick microbiome.
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Affiliation(s)
- Telleasha L Greay
- Vector and Waterborne Pathogens Research Group, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia.
| | - Alexander W Gofton
- Vector and Waterborne Pathogens Research Group, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - Andrea Paparini
- Vector and Waterborne Pathogens Research Group, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - Una M Ryan
- Vector and Waterborne Pathogens Research Group, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - Charlotte L Oskam
- Vector and Waterborne Pathogens Research Group, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - Peter J Irwin
- Vector and Waterborne Pathogens Research Group, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
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89
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Pitta D, Indugu N, Vecchiarelli B, Rico D, Harvatine K. Alterations in ruminal bacterial populations at induction and recovery from diet-induced milk fat depression in dairy cows. J Dairy Sci 2018; 101:295-309. [DOI: 10.3168/jds.2016-12514] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 08/29/2017] [Indexed: 11/19/2022]
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90
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Moussavou-Boundzanga P, Koumakpayi IH, Labouba I, Leroy EM, Belembaogo E, Berthet N. Human papillomavirus detection using the Abbott RealTime high-risk HPV tests compared with conventional nested PCR coupled to high-throughput sequencing of amplification products in cervical smear specimens from a Gabonese female population. Virol J 2017; 14:241. [PMID: 29268766 PMCID: PMC5740888 DOI: 10.1186/s12985-017-0906-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/04/2017] [Indexed: 11/16/2022] Open
Abstract
Background Cervical cancer is the fourth most common malignancy in women worldwide. However, screening with human papillomavirus (HPV) molecular tests holds promise for reducing cervical cancer incidence and mortality in low- and middle-income countries. The performance of the Abbott RealTime High-Risk HPV test (AbRT) was evaluated in 83 cervical smear specimens and compared with a conventional nested PCR coupled to high-throughput sequencing (HTS) to identify the amplicons. Results The AbRT assay detected at least one HPV genotype in 44.57% of women regardless of the grade of cervical abnormalities. Except for one case, good concordance was observed for the genotypes detected with the AbRT assay in the high-risk HPV category determined with HTS of the amplicon generated by conventional nested PCR. Conclusions The AbRT test is an easy and reliable molecular tool and was as sensitive as conventional nested PCR in cervical smear specimens for detection HPVs associated with high-grade lesions. Moreover, sequencing amplicons using an HTS approach effectively identified the genotype of the hrHPV identified with the AbRT test.
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Affiliation(s)
- Pamela Moussavou-Boundzanga
- Centre International de Recherches Médicales de Franceville (CIRMF), Department of Zoonosis and Emerging Diseases, 769, Franceville, BP, Gabon
| | | | - Ingrid Labouba
- Centre International de Recherches Médicales de Franceville (CIRMF), Department of Zoonosis and Emerging Diseases, 769, Franceville, BP, Gabon
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville (CIRMF), Department of Zoonosis and Emerging Diseases, 769, Franceville, BP, Gabon.,Institut de Recherches et de Développement (IRD), Maladies Infectieuses et vecteurs : Ecologie, Génétique, Evolution et Contrôle (IRD 224 - CNRS 5290 6 UM1- UM2), Montpellier, France
| | | | - Nicolas Berthet
- Centre International de Recherches Médicales de Franceville (CIRMF), Department of Zoonosis and Emerging Diseases, 769, Franceville, BP, Gabon. .,Centre National de Recherche Scientifique (CNRS), UMR3569, 25 rue du docteur Roux, 75724, Paris, France. .,Institut Pasteur, Unité Environnement et risques infectieux, Cellule d'Intervention Biologique d'Urgence, 25 rue du Docteur Roux, 75724, Paris, France.
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91
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Watts GS, Youens-Clark K, Slepian MJ, Wolk DM, Oshiro MM, Metzger GS, Dhingra D, Cranmer LD, Hurwitz BL. 16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria. J Appl Microbiol 2017; 123:1584-1596. [PMID: 28940494 PMCID: PMC5765505 DOI: 10.1111/jam.13590] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 06/02/2017] [Accepted: 08/18/2017] [Indexed: 12/20/2022]
Abstract
AIMS Test the choice of 16S rRNA gene amplicon and data analysis method on the accuracy of identification of clinically important bacteria utilizing a benchtop sequencer. METHODS AND RESULTS Nine 16S rRNA amplicons were tested on an Ion Torrent PGM to identify 41 strains of clinical importance. The V1-V2 region identified 40 of 41 isolates to the species level. Three data analysis methods were tested, finding that the Ribosomal Database Project's SequenceMatch outperformed BLAST and the Ion Reporter Metagenomics analysis pipeline. Lastly, 16S rRNA gene sequencing mixtures of four species through a six log range of dilution showed species were identifiable even when present as 0·1% of the mixture. CONCLUSIONS Sequencing the V1-V2 16S rRNA gene region, made possible by the increased read length Ion Torrent PGM sequencer's 400 base pair chemistry, may be a better choice over other commonly used regions for identifying clinically important bacteria. In addition, the SequenceMatch algorithm, freely available from the Ribosomal Database Project, is a good choice for matching filtered reads to organisms. Lastly, 16S rRNA gene sequencing's sensitivity to the presence of a bacterial species at 0·1% of a mixture suggests it has sufficient sensitivity for samples in which important bacteria may be rare. SIGNIFICANCE AND IMPACT OF THE STUDY We have validated 16S rRNA gene sequencing on a benchtop sequencer including simple mixtures of organisms; however, our results highlight deficits for clinical application in place of current identification methods.
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Affiliation(s)
- G S Watts
- The University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.,Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - K Youens-Clark
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ, USA
| | - M J Slepian
- Department of Medicine, University of Arizona, Tucson, AZ, USA.,Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA.,Arizona Center for Accelerated Biomedical Innovation, University of Arizona, Tucson, AZ, USA
| | - D M Wolk
- Pharmaceutical Sciences, Geisinger Health System, Danville, PA, USA.,Center for Infectious Disease Diagnostics and Research, Wilkes University, Geisinger Health System, Danville, PA, USA
| | - M M Oshiro
- The University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA
| | - G S Metzger
- The University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA
| | - D Dhingra
- Life Technologies, Thermo Fisher Scientific, Carlsbad, CA, USA
| | - L D Cranmer
- School of Medicine, Seattle, WA, USA.,University of Washington, Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance, Seattle, WA, USA
| | - B L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ, USA
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92
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Abayasekara LM, Perera J, Chandrasekharan V, Gnanam VS, Udunuwara NA, Liyanage DS, Bulathsinhala NE, Adikary S, Aluthmuhandiram JVS, Thanaseelan CS, Tharmakulasingam DP, Karunakaran T, Ilango J. Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study. BMC Infect Dis 2017; 17:631. [PMID: 28927397 PMCID: PMC5606128 DOI: 10.1186/s12879-017-2727-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/12/2017] [Indexed: 12/27/2022] Open
Abstract
Background Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others. However, to date there has been no commercial application of this technology in infectious disease diagnostic settings. Methods Credence Genomics Rapid Infection Detection™ test, is a molecular based diagnostic test that uses next generation sequencing of bacterial 16S rRNA gene and fungal ITS1 gene region to provide accurate identification of species within a clinical sample. Here we present a study comparing 16S and ITS1 metagenomic identification against conventional culture for clinical samples. Using culture results as gold standard, a comparison was conducted using patient specimens from a clinical microbiology lab. Results Metagenomics based results show a 91.8% concordance rate for culture positive specimens and 52.8% concordance rate with culture negative samples. 10.3% of specimens were also positive for fungal species which was not investigated by culture. Specificity and sensitivity for metagenomics analysis is 91.8 and 52.7% respectively. Conclusion 16S based metagenomic identification of bacterial species within a clinical specimen is on par with conventional culture based techniques and when coupled with clinical information can lead to an accurate diagnostic tool for infectious disease diagnosis. Electronic supplementary material The online version of this article (10.1186/s12879-017-2727-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jennifer Perera
- Dean and Chair Professor of Microbiology, Faculty of Medicine, University of Colombo, P.O. box 271, Colombo, Sri Lanka.,Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Vishvanath Chandrasekharan
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka.,Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Vaz S Gnanam
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Nisala A Udunuwara
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Dileepa S Liyanage
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | | | - Subhashanie Adikary
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | | | | | | | - Tharaga Karunakaran
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
| | - Janahan Ilango
- Credence Genomics Pvt. Ltd, 12 - 3/2, Sunethradevi Road, Kohuwala, Nugegoda, Sri Lanka
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93
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Jamal MAHM, Sharma SP, Chung HJ, Kim HJ, Hong ST, Lee S. Ultra-High Efficient Colony PCR for High Throughput Screening of Bacterial Genes. Indian J Microbiol 2017; 57:365-369. [PMID: 28904423 PMCID: PMC5574782 DOI: 10.1007/s12088-017-0665-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/28/2017] [Indexed: 11/28/2022] Open
Abstract
Current colony PCR methods are not suitable for screening genes encoded in genomic DNA and are limited to E. coli host strains. Here, we describe an ultra-high efficient colony PCR method for high throughput screening of bacterial genes embedded in the genomic DNA of any bacterial species. This new technique expands colony PCR method to several hosts as well as offers a rapid, less expensive and reliable bacterial genomic DNA extraction.
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Affiliation(s)
- Mohammad Abu Hena Mostofa Jamal
- Department of Biomedical Sciences and Institute for Medical Science, Chonbuk National University Medical School, Chonbuk National University, Jeonju, South Korea
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Satya Priya Sharma
- Department of Biomedical Sciences and Institute for Medical Science, Chonbuk National University Medical School, Chonbuk National University, Jeonju, South Korea
| | - Hea-Jong Chung
- Department of Biomedical Sciences and Institute for Medical Science, Chonbuk National University Medical School, Chonbuk National University, Jeonju, South Korea
- Department of Microbiology, Seonam University Medical School, Namwon, Chonbuk 55321 South Korea
| | - Hyeon-Jin Kim
- JINIS BDRD Institute, JINIS Biopharmaceuticals Co., Wanju, Chonbuk Korea
| | - Seong-Tshool Hong
- Department of Biomedical Sciences and Institute for Medical Science, Chonbuk National University Medical School, Chonbuk National University, Jeonju, South Korea
| | - Seungkoo Lee
- Department of Anatomic Pathology, School of Medicine, Kangwon National University Hospital, Kanwong National University, Chuncheon, Gangwon 24341 South Korea
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94
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Avşar C, Civek S, Aras ES. Phenotypic and genotypic characterization of foodborne bacteria isolated from Sinop Province, Turkey. FOOD BIOTECHNOL 2017. [DOI: 10.1080/08905436.2017.1331450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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95
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Ruan L, Wu D, Li X, Huang Q, Lin L, Lin J, Chen L, Xu P, Jin J, Yang N, Li X. Analysis of microbial community composition and diversity in postoperative intracranial infection using high‑throughput sequencing. Mol Med Rep 2017; 16:3938-3946. [PMID: 29067467 PMCID: PMC5646973 DOI: 10.3892/mmr.2017.7082] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 03/28/2017] [Indexed: 02/07/2023] Open
Abstract
Intracranial infection is one of the most serious complications following neurosurgery. It is well acknowledged that bacteria and fungi are the main pathogens responsible for postoperative intracranial infection. However, the microbial community structure, including composition, abundance and diversity, in postoperative intracranial infection is not fully understood, which greatly compromises our understanding of the necessity and effectiveness of postoperative antibiotic treatment. The present study collected eight cerebrospinal fluid (CSF) samples from patients with intracranial infection following neurosurgical procedures. High‑throughput amplicon sequencing for 16S rDNA and internal transcribed spacer (ITS) was performed using the Illumina MiSeq platform to investigate the microbial community composition and diversity between treated and untreated patients. Bioinformatics analysis revealed that the microbial composition and diversity in each patient group (that is, with or without antibiotic treatment) was similar; however, the group receiving antibiotic treatment had a comparatively lower species abundance and diversity compared with untreated patients. At the genus level, Acinetobacter and Staphylococcus were widely distributed in CSF samples from patients with postoperative intracranial infection; in particular, Acinetobacter was detected in all CSF samples. In addition, five ITS fungal libraries were constructed, and Candida was detected in three out of four patients not receiving antibiotic treatment, indicating that the fungal infection should be given more attention. In summary, 16S and ITS high‑throughput amplicon sequencing were practical methods to identify pathogens in the different periods of treatment in patients with postoperative intracranial infection. There was a notable difference in microbial composition and diversity between the treated and untreated patients. Alterations in the microbial community structure may provide a signal whether antibiotic treatment worked in postoperative intracranial infection and may assist surgeons to better control the progression of infection.
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Affiliation(s)
- Lixin Ruan
- Department of Neurosurgery, The People's Hospital of Pingyang, Wenzhou, Zhejiang 325400, P.R. China
| | - Daowu Wu
- Department of Neurosurgery, The People's Hospital of Pingyang, Wenzhou, Zhejiang 325400, P.R. China
| | - Xinchong Li
- Department of Neurosurgery, The People's Hospital of Pingyang, Wenzhou, Zhejiang 325400, P.R. China
| | - Qichuan Huang
- Department of Neurosurgery, The People's Hospital of Pingyang, Wenzhou, Zhejiang 325400, P.R. China
| | - Laipeng Lin
- Department of Neurosurgery, The People's Hospital of Pingyang, Wenzhou, Zhejiang 325400, P.R. China
| | - Jie Lin
- Department of Neurosurgery, The People's Hospital of Pingyang, Wenzhou, Zhejiang 325400, P.R. China
| | - Lie Chen
- Department of Neurosurgery, The People's Hospital of Pingyang, Wenzhou, Zhejiang 325400, P.R. China
| | - Peisong Xu
- Department of Research Service, Zhiyuan Inspection Medical Institute Co., Ltd., Hangzhou, Zhejiang 310006, P.R. China
| | - Jie Jin
- Department of Research Service, Zhiyuan Inspection Medical Institute Co., Ltd., Hangzhou, Zhejiang 310006, P.R. China
| | - Ningmin Yang
- Department of Clinical Laboratory, Zhiyuan Inspection Medical Institute Co., Ltd., Hangzhou, Zhejiang 310006, P.R. China
| | - Xianfeng Li
- Department of Neurosurgery, The People's Hospital of Pingyang, Wenzhou, Zhejiang 325400, P.R. China
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96
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Ames NJ, Ranucci A, Moriyama B, Wallen GR. The Human Microbiome and Understanding the 16S rRNA Gene in Translational Nursing Science. Nurs Res 2017; 66:184-197. [PMID: 28252578 PMCID: PMC5535273 DOI: 10.1097/nnr.0000000000000212] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND As more is understood regarding the human microbiome, it is increasingly important for nurse scientists and healthcare practitioners to analyze these microbial communities and their role in health and disease. 16S rRNA sequencing is a key methodology in identifying these bacterial populations that has recently transitioned from use primarily in research to having increased utility in clinical settings. OBJECTIVES The objectives of this review are to (a) describe 16S rRNA sequencing and its role in answering research questions important to nursing science; (b) provide an overview of the oral, lung, and gut microbiomes and relevant research; and (c) identify future implications for microbiome research and 16S sequencing in translational nursing science. DISCUSSION Sequencing using the 16S rRNA gene has revolutionized research and allowed scientists to easily and reliably characterize complex bacterial communities. This type of research has recently entered the clinical setting, one of the best examples involving the use of 16S sequencing to identify resistant pathogens, thereby improving the accuracy of bacterial identification in infection control. Clinical microbiota research and related requisite methods are of particular relevance to nurse scientists-individuals uniquely positioned to utilize these techniques in future studies in clinical settings.
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Affiliation(s)
- Nancy J Ames
- Nancy J. Ames, RN, PhD, is Clinical Nurse Scientist, Nursing Department, National Institutes of Health Clinical Center, Bethesda, Maryland. Alexandra Ranucci, BS, is MD/MPH Candidate, Tulane University School of Medicine, New Orleans, Louisiana. She was a Post-Baccalaureate Intramural Research Award Recipient, Nursing Department, National Institutes of Health Clinical Center, Bethesda, Maryland, at the time this paper was prepared. Brad Moriyama, PharmD, is Clinical Pharmacist, Pharmacy Department, National Institutes of Health Clinical Center, Bethesda, Maryland. Gwenyth R. Wallen, RN, PhD, is Chief Nurse Officer (Acting), Nursing Department, National Institutes of Health Clinical Center, Bethesda, Maryland
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97
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Yoshioka K, Kakihana K, Doki N, Ohashi K. Gut microbiota and acute graft-versus-host disease. Pharmacol Res 2017; 122:90-95. [PMID: 28576475 DOI: 10.1016/j.phrs.2017.05.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/19/2017] [Accepted: 05/29/2017] [Indexed: 12/12/2022]
Abstract
Although allogeneic stem cell transplantation (allo-SCT) is a potentially curative treatment for various hematological diseases, acute graft-versus-host disease (GVHD) is a major cause of morbidity and mortality, and its management is clinically important. Advances in biological techniques have led to great progress in understanding the complex interactions between the host and the gut microbiota. The gut microbiota clearly modulates the immune response and is associated with the pathogenesis of various disorders. Also in allo-SCT, both preclinical and clinical results indicate that the gut microbiota is closely associated with the development of acute GVHD and transplant outcomes. These results led to the idea that improvement in quantitative and/or qualitative abnormalities of microbiota (dysbiosis) may be a new treatment strategy for acute GVHD. Evaluations of therapies targeting the gut microbiota such as probiotics or fecal microbiota transplantation have just begun. Furthermore, intervention in the gut microbiota with a nutritional approach including prebiotics, postbiotics, and antibiotics selection may also be another promising treatment option for acute GVHD.
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Affiliation(s)
- Kosuke Yoshioka
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Disease Center, Komagome Hospital, Japan
| | - Kazuhiko Kakihana
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Disease Center, Komagome Hospital, Japan.
| | - Noriko Doki
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Disease Center, Komagome Hospital, Japan
| | - Kazuteru Ohashi
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Disease Center, Komagome Hospital, Japan
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98
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Burton EN, Cohn LA, Reinero CN, Rindt H, Moore SG, Ericsson AC. Characterization of the urinary microbiome in healthy dogs. PLoS One 2017; 12:e0177783. [PMID: 28545071 PMCID: PMC5435306 DOI: 10.1371/journal.pone.0177783] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 05/03/2017] [Indexed: 12/31/2022] Open
Abstract
The urinary bladder in healthy dogs has dogmatically been considered free of bacteria. This study used culture independent techniques to characterize the healthy canine urinary microbiota. Urine samples collected by antepubic cystocentesis from dogs without urinary infection were used for DNA extraction. Genital tract and rectal samples were collected simultaneously from the same dogs. The V4 hypervariable region of the 16S rRNA bacterial gene was amplified and compared against Greengenes database for OTU assignment and relative abundance for urine, genital, and rectal samples. After excluding 4 dogs with cultivable bacteria, samples from 10 male (M; 1 intact) and 10 female (F) spayed dogs remained. All samples provided adequate genetic material for analysis. Four taxa (Pseudomonas sp., Acinetobacter sp., Sphingobium sp. and Bradyrhizobiaceae) dominated the urinary microbiota in all dogs of both sexes. These taxa were also detected in the genital swabs of both sexes, while the rectal microbiota differed substantially from the other sample sites. Principal component (PC) analysis of PC1 through PC3 showed overlap of urinary and genital microbiota and a clear separation of rectal swabs from the other sample sites along PC1, which explained 44.94% variation. Surprisingly, the urinary microbiota (mean # OTU 92.6 F, 90.2 M) was significantly richer than the genital (67.8 F, 66.6 M) or rectal microbiota (68.3 F, 71.2 M) (p < 0.0001), with no difference between sexes at any sample site. The canine urinary bladder is not a sterile environment and possesses its own unique and diverse microbiota compared to the rectal and genital microbiota. There was no difference between the sexes at any microbiota sample site (urine, genital, and rectal). The predominant bacterial genus for either sex in the urine and genital tracts was Pseudomonas sp.
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Affiliation(s)
- Erin N. Burton
- Department of Veterinary Pathobiology, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
- * E-mail:
| | - Leah A. Cohn
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
| | - Carol N. Reinero
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
| | - Hans Rindt
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
| | - Stephen G. Moore
- Division of Animal Sciences, University of Missouri College of Agriculture, Food and Natural Resources, Columbia, Missouri, United States of America
| | - Aaron C. Ericsson
- Department of Veterinary Pathobiology, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
- University of Missouri Metagenomics Center (MUMC), Columbia, Missouri, United States of America
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Nshimyimana JP, Freedman AJE, Shanahan P, Chua LCH, Thompson JR. Variation of Bacterial Communities with Water Quality in an Urban Tropical Catchment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5591-5601. [PMID: 28414467 DOI: 10.1021/acs.est.6b04737] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A major challenge for assessment of water quality in tropical environments is the natural occurrence and potential growth of Fecal Indicator Bacteria (FIB). To gain a better understanding of the relationship between measured levels of FIB and the distribution of sewage-associated bacteria, including potential pathogens, in the tropics this study compared the abundance of FIB (Total coliforms and E. coli) and the Bacteroidales (HF183 marker) with bacterial community structure determined by next-generation amplicon sequencing. Water was sampled twice over 6 months from 18 sites within a tropical urban catchment and reservoir, followed by extraction of DNA from microorganisms, and sequencing targeting the V3-V4 region of the 16S rRNA gene. Multivariate statistical analyses indicated that bacterial community composition (BCC) varied between reservoir and catchment, within catchment land-uses, and with E. coli concentration. Beta-regression indicated that the proportion of sequences from sewage-associated taxa (SAT) or pathogen-like sequences (PLS) were predicted most significantly by measured levels of E. coli(log MPN/100 mL) (χ2 > 8.7; p < 0.003). In addition, SAT were significantly predicted by log HF183 levels (χ2=13.1; p = 0.0003) while PLS were not. Our study suggests that measurements of E. coli concentration could be useful in predicting samples enriched in sewage-associated and pathogen-like bacteria in tropical environments despite the potential for nonconservative behavior.
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Affiliation(s)
- Jean Pierre Nshimyimana
- School of Civil and Environmental Engineering, Nanyang Technological University (NTU) , 50 Nanyang Avenue, Singapore 639798, Singapore
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT) , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Centre for Environmental Sensing and Modeling (CENSAM), Singapore-MIT Alliance for Research and Technology (SMART) , 1 Create Way, Singapore 138602, Singapore
- Singapore Center on Environmental Life Sciences Engineering (SCELSE), NTU , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Adam Joshua Ehrich Freedman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT) , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Centre for Environmental Sensing and Modeling (CENSAM), Singapore-MIT Alliance for Research and Technology (SMART) , 1 Create Way, Singapore 138602, Singapore
| | - Peter Shanahan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT) , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Centre for Environmental Sensing and Modeling (CENSAM), Singapore-MIT Alliance for Research and Technology (SMART) , 1 Create Way, Singapore 138602, Singapore
| | - Lloyd C H Chua
- School of Engineering, Deakin University , Waurn Ponds, Geelong, Victoria 3216, Australia
| | - Janelle R Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT) , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Centre for Environmental Sensing and Modeling (CENSAM), Singapore-MIT Alliance for Research and Technology (SMART) , 1 Create Way, Singapore 138602, Singapore
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100
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Bryan A, Kirkpatrick LM, Manaloor JJ, Salipante SJ. 16S rRNA deep sequencing identifies Actinotignum schaalii as the major component of a polymicrobial intra-abdominal infection and implicates a urinary source. JMM Case Rep 2017; 4:e005091. [PMID: 29026619 PMCID: PMC5630961 DOI: 10.1099/jmmcr.0.005091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/23/2017] [Indexed: 11/23/2022] Open
Abstract
Introduction. It can be difficult to catalogue the individual organisms comprising polymicrobial patient infections, both because conventional clinical microbiological culture does not facilitate the isolation and enumeration of all members of a complex microbial community, and because fastidious organisms may be mixed with organisms that grow rapidly in vitro. Empiric antimicrobial treatment is frequently employed based on the anatomical site and the suspected source of the infection, especially when an appropriately collected surgical specimen is not obtained. Case presentation. We present a case of an intra-abdominal infection in a patient with complex anatomy and recurrent urinary tract infections. Imaging did not reveal a clear source of infection, no growth was obtained from urine cultures and initial abdominal fluid cultures were also negative. In contrast, 16S rRNA deep sequencing of abdominal fluid samples revealed mixed bacterial populations with abundant anaerobes, including Actinotignum schaalii (Actinobaculum schaalii). Ultimately, only Enterobacter cloacae complex and meticillin-resistant Staphylococcus aureus, both of which were identified by sequencing, were recovered by culture. Conclusion. The clinical application of 16S rRNA deep sequencing can more comprehensively and accurately define the organisms present in an individual patient's polymicrobial infection than conventional microbiological culture, detecting species that are not recovered under standard culture conditions or that are otherwise unexpected. These results can facilitate effective antimicrobial stewardship and help elucidate the possible origins of infections.
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Affiliation(s)
- Andrew Bryan
- Department of Laboratory Medicine, University of Washington, Box 357110, 1959 NE Pacific Street, NW120, Seattle, WA, USA
| | - Lindsey M Kirkpatrick
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John J Manaloor
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Box 357110, 1959 NE Pacific Street, NW120, Seattle, WA, USA
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