1
|
Fida M, Tande AJ. State-of-the-Art Metagenomic Sequencing and Its Role in the Diagnosis of Periprosthetic Joint Infections. Infect Dis Clin North Am 2024:S0891-5520(24)00062-X. [PMID: 39277504 DOI: 10.1016/j.idc.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
Metagenomic next-generation sequencing (mNGS) is increasingly being recognized as a valuable diagnostic tool for periprosthetic joint infections (PJIs). This study reviews the diagnostic utility of mNGS, highlighting its improved sensitivity in detecting pathogens, particularly in culture-negative and polymicrobial infections. However, the clinical application of this method is hindered by challenges such as the prevalence of host DNA, the necessity for extensive bioinformatic analysis, and the potential for contamination, which can lead to misinterpretation of results. As mNGS continues to evolve, it holds significant potential to improve the management of PJI and enhance the application of precision medicine in orthopedic infections.
Collapse
Affiliation(s)
- Madiha Fida
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Aaron J Tande
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
2
|
Delarbre D, Lavrard P, Elias A, Bossi V, Kacel I, Janvier F, Fournier PE. Bacterial DNA enrichment for low-inoculum fracture-related infection diagnostic using high-throughput sequencing. Diagn Microbiol Infect Dis 2024; 110:116411. [PMID: 39018934 DOI: 10.1016/j.diagmicrobio.2024.116411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 07/19/2024]
Abstract
One of the main barriers for the implementation of metagenomic sequencing in routine diagnosis of infectious diseases is the presence of host DNA. While several enrichment methods are likely to overcome this issue, their effectiveness for specimens such as bone in the case of chronic infections remains to be determined. We compared the relevance of two methods for bacterial DNA enrichment when compared to a reference protocol during pretreatment of bone samples from fracture-related infections before HTS by both Illumina Miseq and Oxford Nanopore Technology (ONT). The bacterial/human DNA ratio was higher for either protocols than the reference technique (p = 0.00012), without any significant difference between them. HTS sensitivity over culture ranged from 21.7 % to 85 %. The ability of the studied protocols to improve the bacterial/human DNA ratio depends on the sequencing technique employed. In this context, there is room for improvement in enhancing the sensitivity of HTS for diagnostic purpose.
Collapse
Affiliation(s)
- David Delarbre
- Division of Internal Medicine and Infectious Diseases, Military Teaching Hospital Sainte-Anne, 2, boulevard Sainte-Anne, BP 600, Cedex 9, 83800, Toulon, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR (VITROME), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
| | - Philippe Lavrard
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR (VITROME), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Antoine Elias
- Centre Hospitalier Intercommunal Toulon - La Seyne sur Mer (C.H.I.T.S.), Toulon, France
| | | | - Idir Kacel
- Institut Méditerranée-Infection, Marseille, France
| | - Fréderic Janvier
- Division of microbiology, Military Teaching Hospital Sainte-Anne, 2, boulevard Sainte-Anne, BP 600, Cedex 9, 83800, Toulon, France
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR (VITROME), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| |
Collapse
|
3
|
Pinto D, Themudo G, Pereira AC, Botelho A, Cunha MV. Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation. Int J Mol Sci 2024; 25:3869. [PMID: 38612679 PMCID: PMC11011339 DOI: 10.3390/ijms25073869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Epidemiological surveillance of animal tuberculosis (TB) based on whole genome sequencing (WGS) of Mycobacterium bovis has recently gained track due to its high resolution to identify infection sources, characterize the pathogen population structure, and facilitate contact tracing. However, the workflow from bacterial isolation to sequence data analysis has several technical challenges that may severely impact the power to understand the epidemiological scenario and inform outbreak response. While trying to use archived DNA from cultured samples obtained during routine official surveillance of animal TB in Portugal, we struggled against three major challenges: the low amount of M. bovis DNA obtained from routinely processed animal samples; the lack of purity of M. bovis DNA, i.e., high levels of contamination with DNA from other organisms; and the co-occurrence of more than one M. bovis strain per sample (within-host mixed infection). The loss of isolated genomes generates missed links in transmission chain reconstruction, hampering the biological and epidemiological interpretation of data as a whole. Upon identification of these challenges, we implemented an integrated solution framework based on whole genome amplification and a dedicated computational pipeline to minimize their effects and recover as many genomes as possible. With the approaches described herein, we were able to recover 62 out of 100 samples that would have otherwise been lost. Based on these results, we discuss adjustments that should be made in official and research laboratories to facilitate the sequential implementation of bacteriological culture, PCR, downstream genomics, and computational-based methods. All of this in a time frame supporting data-driven intervention.
Collapse
Affiliation(s)
- Daniela Pinto
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Gonçalo Themudo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
| | - André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana Botelho
- National Institute for Agrarian and Veterinary Research (INIAV IP), Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| |
Collapse
|
4
|
Ali J, Johansen W, Ahmad R. Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing. Sci Rep 2024; 14:6534. [PMID: 38503770 PMCID: PMC10951244 DOI: 10.1038/s41598-024-55635-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Bloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2-4 days. Early and accurate antibiotic prescription is vital in sepsis to mitigate mortality and antibiotic resistance. This study aimed to reduce the wait time for sepsis diagnosis by employing shorter blood culture incubation times for BD BACTEC™ bottles using standard laboratory incubators, followed by real-time nanopore sequencing and data analysis. The method was tested on nine blood samples spiked with clinical isolates from the six most prevalent sepsis-causing pathogens. The results showed that pathogen identification was possible at as low as 102-104 CFU/mL, achieved after just 2 h of incubation and within 40 min of nanopore sequencing. Moreover, all the antimicrobial resistance genes were identified at 103-107 CFU/mL, achieved after incubation for 5 h and only 10 min to 3 h of sequencing. Therefore, the total turnaround time from sample collection to the information required for an informed decision on the right antibiotic treatment was between 7 and 9 h. These results hold significant promise for better clinical management of sepsis compared with current culture-based methods.
Collapse
Affiliation(s)
- Jawad Ali
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317, Hamar, Norway
| | - Wenche Johansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317, Hamar, Norway.
- Institute of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Hansine Hansens Veg 18, 9019, Tromsø, Norway.
| |
Collapse
|
5
|
Vidal-García M, Urrutikoetxea-Gutiérrez M, Forero Niampira JC, Basaras M, Cisterna R, Díaz de Tuesta Del Arco JL. Ultrafast detection of β-lactamase resistance in Klebsiella pneumoniae from blood culture by nanopore sequencing. Future Microbiol 2023; 18:1309-1317. [PMID: 37850345 DOI: 10.2217/fmb-2023-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/25/2023] [Indexed: 10/19/2023] Open
Abstract
Aim: This study aimed to assess the ultra-fast method using MinION™ sequencing for rapid identification of β-lactamase-producing Klebsiella pneumoniae clinical isolates from positive blood cultures. Methods: Spiked-blood positive blood cultures were extracted using the ultra-fast method and automated DNA extraction for MinION sequencing. Raw reads were analyzed for β-lactamase resistance genes. Multilocus sequence typing and β-lactamase variant characterization were performed after assembly. Results: The ultra-fast method identified clinically relevant β-lactamase resistance genes in less than 1 h. Multilocus sequence typing and β-lactamase variant characterization required 3-6 h. Sequencing quality showed no direct correlation with pore number or DNA concentration. Conclusion: Nanopore sequencing, specifically the ultra-fast method, is promising for the rapid diagnosis of bloodstream infections, facilitating timely identification of multidrug-resistant bacteria in clinical samples.
Collapse
Affiliation(s)
- Matxalen Vidal-García
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
| | - Mikel Urrutikoetxea-Gutiérrez
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
| | - Juan C Forero Niampira
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - Miren Basaras
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - Ramón Cisterna
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - José L Díaz de Tuesta Del Arco
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
| |
Collapse
|
6
|
Quach JU, Diaz MJ, Huda TI, Kinskey JC, Zaman S, Desantis JE, Cios KJ, Blanck G. Bacterial Sequencing Reads in Blood Exome Files from Melanoma and Cervical Cancer Patients are Associated with Cancer Recurrence. Mol Biotechnol 2023; 65:1476-1484. [PMID: 36653589 DOI: 10.1007/s12033-023-00663-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Bacteremia poses great risk for morbidity and mortality for immunocompromised cancer patients. Although the presence of bacteria within solid tumors is gaining greater attention, few studies have analyzed species of bacteria in the blood and their effect on cancer clinical outcomes. Using the Kraken 2 taxonomic profiling tool, we classified bacteria present in blood and primary tumors of cervical cancer and melanoma cases. The Cancer Genome Atlas (TCGA) melanoma blood exome files with Pseudomonas species were found to represent a worse disease-free survival (DFS) probability, while a worse overall survival (OS) result was evidenced for both the TCGA and Moffitt Cancer Center melanoma datasets. Cervical cancer cases with reads representing the Bradyrhizobium genus and Bradyrhizobium sp. BTAi1 found in blood and tumor exome files were found to have lower DFS. Additionally, reduced DFS and OS were observed for cervical cancer cases positive for Bacteroides species including Bacteroides fragilis. This study provides novel evidence and a novel approach for indicating that bacteria in blood is associated with cancer recurrence. These findings may guide the development of more efficient prognostic and screening tools related to bacterial blood infections of melanoma and cervical cancer patients.
Collapse
Affiliation(s)
- Jessica U Quach
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Michael J Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Jacob C Kinskey
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Saif Zaman
- Department of Internal Medicine, Yale University, New Haven, CT, 06520, USA
| | - John E Desantis
- Research Computing, University of South Florida, Tampa, FL, 33620, USA
| | - Konrad J Cios
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA.
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
| |
Collapse
|
7
|
Peterson SW, Demczuk W, Martin I, Adam H, Bharat A, Mulvey MR. Identification of bacterial and fungal pathogens directly from clinical blood cultures using whole genome sequencing. Genomics 2023; 115:110580. [PMID: 36792020 DOI: 10.1016/j.ygeno.2023.110580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 01/17/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
Bloodstream infections are a major cause of morbidity and mortality worldwide. Early administration of appropriate antimicrobial therapy can improve patient survival and prevent antimicrobial resistance (AMR). Whole genome sequencing (WGS) can provide information for pathogen identification, AMR prediction and sequence typing earlier than current phenotypic diagnostic methods. WGS was performed on 97 clinical blood specimens and matched culture isolate pairs. Specimen/isolate pairs were MLST sequence-typed and further characterization was performed on Streptococcus species. WGS correctly identified 91.7% of clinical specimens and 93.2% of matched isolates representing 35 different microbial species. MLST types were assigned for 89.9% of matched cultures and 21.7% of blood specimens, with higher success for blood culture specimens extracted within 3 days (52% characterized) than 7 days (9.3%). This study demonstrates the potential use of WGS for identification and characterization of pathogens directly from blood culture specimens to facilitate timely initiation of appropriate antimicrobial therapies.
Collapse
Affiliation(s)
- S W Peterson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - W Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - I Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - H Adam
- Diagnostic Services, Shared Health Manitoba, Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - A Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| | - M R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| |
Collapse
|
8
|
Ahmadi A, Khezri A, Nørstebø H, Ahmad R. A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk. Front Microbiol 2023; 13:1104701. [PMID: 36687564 PMCID: PMC9852903 DOI: 10.3389/fmicb.2022.1104701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a unique opportunity to study the microbial community and antimicrobial resistance (AMR) in mastitis. However, the complexity of milk samples and the presence of a high amount of host DNA in milk from infected udders often make this very challenging. Methods Here, we tested 24 bovine milk samples (18 mastitis and six non-mastitis) using four different commercial kits (Qiagens' DNeasy® PowerFood® Microbial, Norgens' Milk Bacterial DNA Isolation, and Molzyms' MolYsis™ Plus and Complete5) in combination with filtration, low-speed centrifugation, nuclease, and 10% bile extract of male bovine (Ox bile). Isolated DNA was quantified, checked for the presence/absence of host and pathogen using PCR and sequenced using MinION nanopore sequencing. Bioinformatics analysis was performed for taxonomic classification and antimicrobial resistance gene detection. Results The results showed that kits designed explicitly for bacterial DNA isolation from food and dairy matrices could not deplete/minimize host DNA. Following using MolYsis™ Complete 5 + 10% Ox bile + micrococcal nuclease combination, on average, 17% and 66.5% of reads were classified as bovine and Staphylococcus aureus reads, respectively. This combination also effectively enriched other mastitis pathogens, including Escherichia coli and Streptococcus dysgalactiae. Furthermore, using this approach, we identified important AMR genes such as Tet (A), Tet (38), fosB-Saur, and blaZ. We showed that even 40 min of the MinION run was enough for bacterial identification and detecting the first AMR gene. Conclusion We implemented an effective method (sensitivity of 100% and specificity of 92.3%) for host DNA removal and bacterial DNA enrichment (both gram-negative and positive) directly from bovine mastitis milk. To the best of our knowledge, this is the first culture- and amplification-independent study using nanopore-based metagenomic sequencing for real-time detection of the pathogen (within 5 hours) and the AMR profile (within 5-9 hours), in mastitis milk samples. These results provide a promising and potential future on-farm adaptable approach for better clinical management of mastitis.
Collapse
Affiliation(s)
- Asal Ahmadi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway,Institute of Clinical Medicine, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway,*Correspondence: Rafi Ahmad,
| |
Collapse
|
9
|
Pallerla SR, Van Dong D, Linh LTK, Van Son T, Quyen DT, Hoan PQ, Trung NT, The NT, Rüter J, Boutin S, Nurjadi D, Sy BT, Kremsner PG, Meyer CG, Song LH, Velavan TP. Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting. Ann Clin Microbiol Antimicrob 2022; 21:39. [PMID: 36064402 PMCID: PMC9443622 DOI: 10.1186/s12941-022-00530-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/11/2022] [Indexed: 11/21/2022] Open
Abstract
Aim The aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise. Methods DNA was isolated from the cerebrospinal fluid (CSF) of 30 patients with suspected bacterial meningitis. The isolated DNA was subjected to 16S sequencing using MinION™. The data were analysed in real time via the EPI2ME cloud platform. The Nanopore sequencing was done in parallel to routine microbiological diagnostics. Results Nanopore sequencing detected bacterial pathogens to species level in 13 of 30 (43%) samples. CSF culture showed 40% (12/30) positivity. In 21 of 30 patients (70%) with suspected bacterial meningitis, both methods yielded concordant results. About nine of 30 samples showed discordant results, of these five were false positive and four were false negative. In five of the culture negative results, nanopore sequencing was able to detect pathogen genome, due to the higher sensitivity of the molecular diagnostics. In two other samples, the CSF culture revealed Cryptococcus neoformans and Streptococcus pneumoniae, which were not detected by Nanopore sequencing. Overall, using both the cultures and 16S Nanopore sequencing, positivity rate increased from 40% (12/30) to 57% (17/30). Conclusion Next-generation sequencing could detect pathogens within six hours and could become an important tool for both pathogen screening and surveillance in low- and middle-income countries (LMICs) that do not have direct access to extensive bioinformatics expertise. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-022-00530-6.
Collapse
Affiliation(s)
- Srinivas Reddy Pallerla
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany
| | - Do Van Dong
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Le Thi Kieu Linh
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Trinh Van Son
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Dao Thanh Quyen
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Phan Quoc Hoan
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Ngo Tat Trung
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Nguyen Trong The
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Jule Rüter
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Bui Tien Sy
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.,Department of Microbiology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Peter G Kremsner
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Christian G Meyer
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Le Huu Song
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam. .,108 Military Central Hospital, Hanoi, Vietnam.
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany. .,Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.
| |
Collapse
|
10
|
Target-enriched sequencing enables accurate identification of bloodstream infections in whole blood. J Microbiol Methods 2021; 192:106391. [PMID: 34915067 DOI: 10.1016/j.mimet.2021.106391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022]
Abstract
Bloodstream infections are within the top ten causes of death globally, with a mortality rate of up to 70%. Gold standard blood culture testing is time-consuming, resulting in delayed, but accurate, treatment. Molecular methods, such as RT-qPCR, have limited targets in one run. We present a new Ampliseq detection system (ADS) combining target amplification and next-generation sequencing for accurate identification of bacteria, fungi, and antimicrobial resistance determinants directly from blood samples. In this study, we included removal of human genomic DNA during nucleic acid extraction, optimized the target sequence set and drug resistance genes, performed antimicrobial resistance profiling of clinical isolates, and evaluated mock specimens and clinical samples by ADS. ADS successfully identified pathogens at the species-level in 36 h, from nucleic acid extraction to results. Besides pathogen identification, ADS can also present drug resistance profiles. ADS enabled detection of all bacteria and accurate identification of 47 pathogens. In 20 spiked samples and 8 clinical specimens, ADS detected at least 92.81% of reads mapped to pathogens. ADS also showed consistency with the three culture-negative samples, and correctly identified pathogens in four of five culture-positive clinical blood specimens. This Ampliseq-based technology promises broad coverage and accurate pathogen identification, helping clinicians to accurately diagnose and treat bloodstream infections.
Collapse
|
11
|
Sanabria AM, Janice J, Hjerde E, Simonsen GS, Hanssen AM. Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles. Sci Rep 2021; 11:20848. [PMID: 34675288 PMCID: PMC8531021 DOI: 10.1038/s41598-021-00383-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/08/2021] [Indexed: 11/20/2022] Open
Abstract
Shotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with periprosthetic tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known periprosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209 ×. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis approach clearly influenced the results, i.e. read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data.
Collapse
Affiliation(s)
- Adriana Maria Sanabria
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Jessin Janice
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Norwegian Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Centre for Bioinformatics, Department of Chemistry, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Gunnar Skov Simonsen
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anne-Merethe Hanssen
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.
| |
Collapse
|
12
|
Metagenomic Sequencing as a Pathogen-Agnostic Clinical Diagnostic Tool for Infectious Diseases: a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies. J Clin Microbiol 2021; 59:e0291620. [PMID: 33910965 DOI: 10.1128/jcm.02916-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Metagenomic sequencing is frequently claimed to have the potential to revolutionize microbiology through rapid species identification and antimicrobial resistance (AMR) prediction. We assess the progress toward these developments. We perform a systematic review and meta-analysis of all published literature on culture-independent metagenomic sequencing for pathogen-agnostic infectious disease diagnostics up to 12 August 2020. Methodologic bias and applicability were assessed using the tool Quadas-2. (Prospero CRD42020163777). A total of 2,023 clinical samples from 13/21 eligible diagnostic test accuracy studies were included in the meta-analysis. Reference standards were culture, molecular testing, clinical decision, or a composite measure. Sensitivity and specificity in the most widely investigated sample types were 90% (95% confidence interval [CI], 78% to 96%) and 86% (45% to 98%) for blood, 75% (54% to 89%) and 96% (72% to 100%) for cerebrospinal fluid (CSF), and 84% (79% to 88%) and 67% (38% to 87%) for orthopedic samples, respectively. We identified a limited use of controls, especially negative controls which were used in only 62% (13/21) of studies. AMR prediction and comparison to phenotypic results were undertaken in four studies; categorical agreement was 88%(80% to 97%), and very major and major error rates were 24% (8% to 40%) and 5% (0% to 12%), respectively. Better human DNA depletion methods are required; a median 91% (interquartile range [IQR], 82% to 98%; range, 76% to 98%) of sequences was classified as human. The median (IQR; range) time from sample to result was 29 hours (24 to 94; 4 to 144 hours). The reported consumable cost per sample ranged from $130 to $685. There is scope for improving the quality of reporting in clinical metagenomic studies. Although our results are limited by the heterogeneity displayed, our results reflect a promising outlook for clinical metagenomics. Methodological improvements and convergence around protocols and best practices may improve performance in the future.
Collapse
|
13
|
Chew KL, Octavia S, Jureen R, Lin RTP, Teo JWP. Targeted amplification and MinION nanopore sequencing of key azole and echinocandin resistance determinants of clinically relevant Candida spp. from blood culture bottles. Lett Appl Microbiol 2021; 73:286-293. [PMID: 34060660 DOI: 10.1111/lam.13516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/29/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022]
Abstract
The objective of the study was to evaluate the use of targeted multiplex Nanopore MinION amplicon re-sequencing of key Candida spp. from blood culture bottles to identify azole and echinocandin resistance associated SNPs. Targeted PCR amplification of azole (ERG11 and ERG3) and echinocandin (FKS) resistance-associated loci was performed on positive blood culture media. Sequencing was performed using MinION nanopore device with R9.4.1 Flow Cells. Twenty-eight spiked blood cultures (ATCC strains and clinical isolates) and 12 prospectively collected positive blood cultures with candidaemia were included. Isolate species included Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis and Candida auris. SNPs that were identified on ERG and FKS genes using Snippy tool and CLC Genomic Workbench were correlated with phenotypic testing by broth microdilution (YeastOne™ Sensititre). Illumina whole-genome-sequencing and Sanger-sequencing were also performed as confirmatory testing of the mutations identified from nanopore sequencing data. There was a perfect agreement of the resistance-associated mutations detected by MinION-nanopore-sequencing compared to phenotypic testing for acquired resistance (16 with azole resistance; 3 with echinocandin resistance), and perfect concordance of the nanopore sequence mutations to Illumina and Sanger data. Mutations with no known association with phenotypic drug resistance and novel mutations were also detected.
Collapse
Affiliation(s)
- K L Chew
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - S Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - R Jureen
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - R T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - J W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore
| |
Collapse
|
14
|
Zhou M, Wu Y, Kudinha T, Jia P, Wang L, Xu Y, Yang Q. Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing. Front Genet 2021; 12:620009. [PMID: 33841495 PMCID: PMC8024499 DOI: 10.3389/fgene.2021.620009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Bloodstream infection is a major cause of morbidity and mortality worldwide. We explored whether MinION nanopore sequencing could accelerate diagnosis, resistance, and virulence profiling prediction in simulated blood samples and blood cultures. One milliliter of healthy blood samples each from direct spike (sample 1), anaerobic (sample 2), and aerobic (sample 3) blood cultures with initial inoculation of ∼30 CFU/ml of a clinically isolated Klebsiella pneumoniae strain was subjected to DNA extraction and nanopore sequencing. Hybrid assembly of Illumina and nanopore reads from pure colonies of the isolate (sample 4) was used as a reference for comparison. Hybrid assembly of the reference genome identified a total of 39 antibiotic resistance genes and 77 virulence genes through alignment with the CARD and VFDB databases. Nanopore correctly detected K. pneumoniae in all three blood samples. The fastest identification was achieved within 8 h from specimen to result in sample 1 without blood culture. However, direct sequencing in sample 1 only identified seven resistance genes (20.6%) but 28 genes in samples 2–4 (82.4%) compared to the reference within 2 h of sequencing time. Similarly, 11 (14.3%) and 74 (96.1%) of the virulence genes were detected in samples 1 and 2–4 within 2 h of sequencing time, respectively. Direct nanopore sequencing from positive blood cultures allowed comprehensive pathogen identification, resistance, and virulence genes prediction within 2 h, which shows its promising use in point-of-care clinical settings.
Collapse
Affiliation(s)
- Menglan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yarong Wu
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW, Australia.,Pathology West, NSW Health Pathology, Orange, NSW, Australia
| | - Peiyao Jia
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Wang
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
15
|
Sanabria A, Hjerde E, Johannessen M, Sollid JE, Simonsen GS, Hanssen AM. Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study. Front Microbiol 2020; 11:1687. [PMID: 32765476 PMCID: PMC7380264 DOI: 10.3389/fmicb.2020.01687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/29/2020] [Indexed: 01/19/2023] Open
Abstract
Clinical metagenomics is actively moving from research to clinical laboratories. It has the potential to change the microbial diagnosis of infectious diseases, especially when detection and identification of pathogens can be challenging, such as in prosthetic joint infection (PJI). The application of metagenomic sequencing to periprosthetic joint tissue (PJT) specimens is often challenged by low bacterial load in addition to high level of inhibitor and contaminant host DNA, limiting pathogen recovery. Shotgun-metagenomics (SMg) performed directly on positive blood culture bottles (BCBs) inoculated with PJT may be a convenient approach to overcome these obstacles. The aim was to test if it is possible to perform SMg on PJT inoculated into BCBs for pathogen identification in PJI diagnosis. Our study was conducted as a laboratory method development. For this purpose, spiked samples (positive controls), negative control and clinical tissue samples (positive BCBs) were included to get a comprehensive overview. We developed a method for preparation of bacterial DNA directly from PJT inoculated in BCBs. Samples were processed using MolYsis5 kit for removal of human DNA and DNA extracted with BiOstic kit. High DNA quantity/quality was obtained, and no inhibition was observed during the library preparation, allowing further sequencing process. DNA sequencing reads obtained from the BCBs, presented a low proportion of human reads (<1%) improving the sensitivity of bacterial detection. We detected a 19-fold increase in the number of reads mapping to human in a sample untreated with MolYsis5. Taxonomic classification of clinical samples identified a median of 96.08% (IQR, 93.85-97.07%; range 85.7-98.6%) bacterial reads. Shotgun-metagenomics results were consistent with the results from a conventional BCB culture method, validating our approach. Overall, we demonstrated a proof of concept that it is possible to perform SMg directly on BCBs inoculated with PJT, with potential of pathogen identification in PJI diagnosis. We consider this a first step in research efforts needed to face the challenges presented in PJI diagnoses.
Collapse
Affiliation(s)
- Adriana Sanabria
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry, Centre for Bioinformatics, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Mona Johannessen
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Johanna Ericson Sollid
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Gunnar Skov Simonsen
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of Norway, Tromsø, Norway
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anne-Merethe Hanssen
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
16
|
Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing. Sci Rep 2020; 10:7622. [PMID: 32376847 PMCID: PMC7203151 DOI: 10.1038/s41598-020-64616-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/20/2020] [Indexed: 12/27/2022] Open
Abstract
Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1-2 days for identification of bacterial agent and an additional 2-3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and blaCTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes.
Collapse
|
17
|
Epidemiology of two decades of invasive meningococcal disease in the Republic of Ireland: an analysis of national surveillance data on laboratory-confirmed cases from 1996 to 2016. Epidemiol Infect 2020; 147:e142. [PMID: 30869045 PMCID: PMC6518514 DOI: 10.1017/s0950268819000396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We examined the epidemiology of invasive meningococcal disease (IMD) in the Republic of Ireland (ROI) between epidemiological year (EY) 1996/1997 and EY2015/2016. Over the 20 EYs, 3707 cases were reported with annual incidence rates per 100 000 peaking at 11.6 in EY1999/2000, decreasing significantly to 1.5 in EY2015/2016. The highest disease burden was in infants and children <5, whereas adults aged ⩾65 years experienced the highest case fatality ratio (CFR) of 15.7% but over the study period the median annual CFR remained low (4.4%). Meningococcal serogroup B (menB) dominated (78%), followed by menC (17%), menW (1%) and menY (1%). The incidence of menC IMD declined significantly in all age groups after menC vaccine introduction in 2000. MenB incidence also declined over the 20 EYs with decreasing trends in all age groups under 65, including an almost 50% decrease in infants over the final four EYs. IMD incidence in the ROI has declined, partly attributable to menC vaccination success, coupled with a spontaneous decline in menB. However, recent gradual increases in non-menB IMD and the introduction of vaccines targeting menB demand continued detailed surveillance to accurately monitor trends and to assess vaccine impact.
Collapse
|
18
|
An identification protocol for ESBL-producing Gram-negative bacteria bloodstream infections using a MinION nanopore sequencer. J Med Microbiol 2019; 68:1219-1226. [PMID: 31237534 DOI: 10.1099/jmm.0.001024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The new third-generation sequencing platform MinION is an attractive maintenance-free and disposable portable tool that can perform long-read and real-time sequencing. In this study, we validated this technology for the identification of pathogens from positive blood culture (BC) bottles. METHODOLOGY A total of 38 positive BC bottles were collected from patients with bloodstream infections, and 18 isolates of Gram-negative (GN) bacteria and 20 isolates of Gram-positive (GP) bacteria were identified from these using 16S rRNA sequencing and then used in this study. DNA was extracted from each aliquot using an extraction protocol that combined glass bead beating and chemical lysis. Up to 200 ng of each purified DNA sample was processed for library preparation and whole-genome sequencing was performed on up to 12 samples through a single MinION flow cell. RESULTS All GN bacteria identifications made by MinION sequencing for 30 min using the What's In My Pot? (WIMP) workflow via EPI2ME on the basis of the most frequent classified reads were consistent with those made by 16S rRNA sequencing. On the other hand, for GP bacteria specimens, the identification results for 16S rRNA sequencing and MinION were only in agreement in 12 out of 20 (60.0 %) cases. ARMA analysis was able to detect extended-spectrum β-lactamase (ESBL)-associated genes among various antimicrobial resistance-related genes. CONCLUSION We demonstrated the potential of the MinION sequencer for the identification of GN bacteria from positive BC bottles and the confirmation of an ESBL phenotype. This innovative sequence technology and its application could lead to a breakthrough in the diagnosis of infectious diseases.
Collapse
|
19
|
Franch O, Han X, Marcussen LB, Givskov A, Andersen MB, Godbole AA, Harmsen C, Nørskov-Lauritsen N, Thomsen J, Pedersen FS, Wang Y, Shi D, Wejse C, Pødenphant L, Nagaraja V, Bertl J, Stougaard M, Ho YP, Hede MS, Labouriau R, Knudsen BR. A new DNA sensor system for specific and quantitative detection of mycobacteria. NANOSCALE 2019; 11:587-597. [PMID: 30556557 DOI: 10.1039/c8nr07850e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the current study, we describe a novel DNA sensor system for specific and quantitative detection of mycobacteria, which is the causative agent of tuberculosis. Detection is achieved by using the enzymatic activity of the mycobacterial encoded enzyme topoisomerase IA (TOP1A) as a biomarker. The presented work is the first to describe how the catalytic activities of a member of the type IA family of topoisomerases can be exploited for specific detection of bacteria. The principle for detection relies on a solid support anchored DNA substrate with dual functions namely: (1) the ability to isolate mycobacterial TOP1A from crude samples and (2) the ability to be converted into a closed DNA circle upon reaction with the isolated enzyme. The DNA circle can act as a template for rolling circle amplification generating a tandem repeat product that can be visualized at the single molecule level by fluorescent labelling. This reaction scheme ensures specific, sensitive, and quantitative detection of the mycobacteria TOP1A biomarker as demonstrated by the use of purified mycobacterial TOP1A and extracts from an array of non-mycobacteria and mycobacteria species. When combined with mycobacteriophage induced lysis as a novel way of effective yet gentle extraction of the cellular content from the model Mycobacterium smegmatis, the DNA sensor system allowed detection of mycobacteria in small volumes of cell suspensions. Moreover, it was possible to detect M. smegmatis added to human saliva. Depending on the composition of the sample, we were able to detect 0.6 or 0.9 million colony forming units (CFU) per mL of mycobacteria, which is within the range of clinically relevant infection numbers. We, therefore, believe that the presented assay, which relies on techniques that can be adapted to limited resource settings, may be the first step towards the development of a new point-of-care diagnostic test for tuberculosis.
Collapse
Affiliation(s)
- Oskar Franch
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Ashikawa S, Tarumoto N, Imai K, Sakai J, Kodana M, Kawamura T, Ikebuchi K, Murakami T, Mitsutake K, Maesaki S, Maeda T. Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer. J Med Microbiol 2018; 67:1589-1595. [PMID: 30311873 DOI: 10.1099/jmm.0.000855] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Bloodstream infections are major causes of morbidity and mortality that lead to prolonged hospital stays and higher medical costs. In this study, we aimed to evaluate the MinION nanopore sequencer for the identification of the most dominant pathogens in positive blood culture bottles. METHODOLOGY 16S and ITS1-5.8S-ITS2 rRNA genes were amplified by PCR reactions with barcoded primers using nine clinical isolates obtained from positive blood bottles and 11 type strains, including five types of Candida species. Barcoded amplicons were mixed, and multiplex sequencing with the MinION sequencer was performed. In addition, barcoded PCR amplicons were sequenced by Sanger sequencing to validate the performance of the MinION. RESULTS The bacterial and Candida spp. identified by MinION sequencing, based on the highest homology of reference sequences from the NCBI gene databases, agreed with the matrix-assisted laser desorption ionization time of flight mass spectrometry results, excepting the closely related species Streptococcusand Escherichia coli. The 'pass' reads obtained within about 10 min of sequencing were sufficient to identify the pathogens. The average values of sequence identities with 1D2 chemistry and the R9.5 flow cell were around 99 %; thus, frequent sequence errors did not affect species identification based on amplicon sequencing. CONCLUSION We have established a rapid, portable and economical technique for the identification of pathogens in positive blood culture bottles through a novel MinION nanopore sequencer amplicon sequencing scheme, which replaces traditional Sanger sequencing.
Collapse
Affiliation(s)
- Sae Ashikawa
- 1School of Medical Technology, Faculty of Health and Medical Care, Saitama Medical University, Saitama, Japan
| | - Norihito Tarumoto
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Kazuo Imai
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Jun Sakai
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Masahiro Kodana
- 4Clinical Laboratory Medicine, Saitama Medical University Hospital, Saitama, Japan
| | - Toru Kawamura
- 4Clinical Laboratory Medicine, Saitama Medical University Hospital, Saitama, Japan
| | - Kenji Ikebuchi
- 4Clinical Laboratory Medicine, Saitama Medical University Hospital, Saitama, Japan
| | - Takashi Murakami
- 3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,5Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Kotaro Mitsutake
- 3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,6Department of Infectious Diseases and Infection Control, International Medical Center, Saitama Medical University, Saitama, Japan
| | - Shigefumi Maesaki
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Takuya Maeda
- 3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,5Department of Microbiology, Saitama Medical University, Saitama, Japan
| |
Collapse
|
21
|
Lowering the Barriers to Routine Whole-Genome Sequencing of Bacteria in the Clinical Microbiology Laboratory. J Clin Microbiol 2018; 56:JCM.00813-18. [PMID: 29950328 DOI: 10.1128/jcm.00813-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Whole-genome sequencing of bacterial isolates is increasingly being used to predict antibacterial susceptibility and resistance. Mason and coauthors describe the phenotypic susceptibility interpretations of more than 1,300 Staphylococcus aureus isolates tested against a dozen antistaphylococcal agents, and they compared these findings to susceptibility predictions made by analyzing whole-genome sequence data (J Clin Microbiol 56:e01815-17, 2018, https://doi.org/10.1128/JCM.01815-17). The genotype-phenotype susceptibility interpretations correlated in 96.3% (2,720/2,825) of resistant findings and 98.8% (11,504/11,639) of susceptible findings. This work by Mason and colleagues is helping to lower the barriers to using whole-genome sequencing of S. aureus in clinical microbiology practice.
Collapse
|