Nanopore-based targeted sequencing test for direct tuberculosis identification, genotyping, and detection of drug resistance mutations: a side-by-side comparison of targeted next-generation sequencing technologies
We investigated the performance of the targeted next-generation sequencing (tNGS)-based Oxford Nanopore Diagnostics AmPORE TB assay, recently approved by the World Health Organization (WHO) as tuberculosis (TB) diagnostic test for the detection of drug resistance on respiratory specimens. A total of...
Uloženo v:
| Vydáno v: | Journal of clinical microbiology Ročník 62; číslo 10; s. e0081524 |
|---|---|
| Hlavní autoři: | , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
United States
16.10.2024
|
| Témata: | |
| ISSN: | 1098-660X, 1098-660X |
| On-line přístup: | Zjistit podrobnosti o přístupu |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | We investigated the performance of the targeted next-generation sequencing (tNGS)-based Oxford Nanopore Diagnostics AmPORE TB assay, recently approved by the World Health Organization (WHO) as tuberculosis (TB) diagnostic test for the detection of drug resistance on respiratory specimens. A total of 104 DNA samples from Xpert MTB/RIF-positive TB sputum specimens were tested using the AmPORE TB kit, with the GenoScreen Deeplex Myc-TB as a comparative tNGS assay. For AmPORE TB, DNA samples were divided into five sequencing runs on the MinION device. Data analysis was performed using proprietary software. The WHO catalog of mutations was used for drug resistance interpretation. The assay achieved a high validity rate of 98% (102/104 DNA samples), homogeneous mean reads coverage across TB-positive specimens, and 100% positive and negative agreements for detecting mutations associated with resistance to rifampicin, pyrazinamide, fluoroquinolones, ethambutol, and capreomycin compared with Deeplex Myc-TB. The main discrepancies for the remaining drugs were attributable to the different assay panel designs. The AmPORE TB turnaround time was approximately 5-6 hours from extracted DNA to tNGS reporting for batches of 22 DNA samples. The AmPORE TB assay drastically reduced the time to tNGS reporting from days to hours and showed good performance for drug-resistant TB profiling compared with Deeplex Myc-TB.
Targeted next-generation sequencing (tNGS) of
provides comprehensive resistance predictions matched to new multidrug-resistant/rifampicin-resistant tuberculosis regimens and received World Health Organization approval for clinical use in respiratory samples in 2024. The advanced version of the Oxford Nanopore Diagnostics AmPORE TB tNGS kit was evaluated in this study for the first time and demonstrated good performance, flexibility, and faster turnaround time compared with the existing solutions. |
|---|---|
| AbstractList | We investigated the performance of the targeted next-generation sequencing (tNGS)-based Oxford Nanopore Diagnostics AmPORE TB assay, recently approved by the World Health Organization (WHO) as tuberculosis (TB) diagnostic test for the detection of drug resistance on respiratory specimens. A total of 104 DNA samples from Xpert MTB/RIF-positive TB sputum specimens were tested using the AmPORE TB kit, with the GenoScreen Deeplex Myc-TB as a comparative tNGS assay. For AmPORE TB, DNA samples were divided into five sequencing runs on the MinION device. Data analysis was performed using proprietary software. The WHO catalog of mutations was used for drug resistance interpretation. The assay achieved a high validity rate of 98% (102/104 DNA samples), homogeneous mean reads coverage across TB-positive specimens, and 100% positive and negative agreements for detecting mutations associated with resistance to rifampicin, pyrazinamide, fluoroquinolones, ethambutol, and capreomycin compared with Deeplex Myc-TB. The main discrepancies for the remaining drugs were attributable to the different assay panel designs. The AmPORE TB turnaround time was approximately 5-6 hours from extracted DNA to tNGS reporting for batches of 22 DNA samples. The AmPORE TB assay drastically reduced the time to tNGS reporting from days to hours and showed good performance for drug-resistant TB profiling compared with Deeplex Myc-TB.
Targeted next-generation sequencing (tNGS) of
provides comprehensive resistance predictions matched to new multidrug-resistant/rifampicin-resistant tuberculosis regimens and received World Health Organization approval for clinical use in respiratory samples in 2024. The advanced version of the Oxford Nanopore Diagnostics AmPORE TB tNGS kit was evaluated in this study for the first time and demonstrated good performance, flexibility, and faster turnaround time compared with the existing solutions. We investigated the performance of the targeted next-generation sequencing (tNGS)-based Oxford Nanopore Diagnostics AmPORE TB assay, recently approved by the World Health Organization (WHO) as tuberculosis (TB) diagnostic test for the detection of drug resistance on respiratory specimens. A total of 104 DNA samples from Xpert MTB/RIF-positive TB sputum specimens were tested using the AmPORE TB kit, with the GenoScreen Deeplex Myc-TB as a comparative tNGS assay. For AmPORE TB, DNA samples were divided into five sequencing runs on the MinION device. Data analysis was performed using proprietary software. The WHO catalog of mutations was used for drug resistance interpretation. The assay achieved a high validity rate of 98% (102/104 DNA samples), homogeneous mean reads coverage across TB-positive specimens, and 100% positive and negative agreements for detecting mutations associated with resistance to rifampicin, pyrazinamide, fluoroquinolones, ethambutol, and capreomycin compared with Deeplex Myc-TB. The main discrepancies for the remaining drugs were attributable to the different assay panel designs. The AmPORE TB turnaround time was approximately 5-6 hours from extracted DNA to tNGS reporting for batches of 22 DNA samples. The AmPORE TB assay drastically reduced the time to tNGS reporting from days to hours and showed good performance for drug-resistant TB profiling compared with Deeplex Myc-TB.We investigated the performance of the targeted next-generation sequencing (tNGS)-based Oxford Nanopore Diagnostics AmPORE TB assay, recently approved by the World Health Organization (WHO) as tuberculosis (TB) diagnostic test for the detection of drug resistance on respiratory specimens. A total of 104 DNA samples from Xpert MTB/RIF-positive TB sputum specimens were tested using the AmPORE TB kit, with the GenoScreen Deeplex Myc-TB as a comparative tNGS assay. For AmPORE TB, DNA samples were divided into five sequencing runs on the MinION device. Data analysis was performed using proprietary software. The WHO catalog of mutations was used for drug resistance interpretation. The assay achieved a high validity rate of 98% (102/104 DNA samples), homogeneous mean reads coverage across TB-positive specimens, and 100% positive and negative agreements for detecting mutations associated with resistance to rifampicin, pyrazinamide, fluoroquinolones, ethambutol, and capreomycin compared with Deeplex Myc-TB. The main discrepancies for the remaining drugs were attributable to the different assay panel designs. The AmPORE TB turnaround time was approximately 5-6 hours from extracted DNA to tNGS reporting for batches of 22 DNA samples. The AmPORE TB assay drastically reduced the time to tNGS reporting from days to hours and showed good performance for drug-resistant TB profiling compared with Deeplex Myc-TB.Targeted next-generation sequencing (tNGS) of Mycobacterium tuberculosis provides comprehensive resistance predictions matched to new multidrug-resistant/rifampicin-resistant tuberculosis regimens and received World Health Organization approval for clinical use in respiratory samples in 2024. The advanced version of the Oxford Nanopore Diagnostics AmPORE TB tNGS kit was evaluated in this study for the first time and demonstrated good performance, flexibility, and faster turnaround time compared with the existing solutions.IMPORTANCETargeted next-generation sequencing (tNGS) of Mycobacterium tuberculosis provides comprehensive resistance predictions matched to new multidrug-resistant/rifampicin-resistant tuberculosis regimens and received World Health Organization approval for clinical use in respiratory samples in 2024. The advanced version of the Oxford Nanopore Diagnostics AmPORE TB tNGS kit was evaluated in this study for the first time and demonstrated good performance, flexibility, and faster turnaround time compared with the existing solutions. |
| Author | Batignani, Virginia Morgan, Godstime Stephen Kojo Cirillo, Daniela Maria Moghaddasi, Kiarash Di Marco, Federico Cabibbe, Andrea Maurizio |
| Author_xml | – sequence: 1 givenname: Andrea Maurizio orcidid: 0000-0001-9727-6465 surname: Cabibbe fullname: Cabibbe, Andrea Maurizio organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 2 givenname: Kiarash orcidid: 0009-0001-0144-0759 surname: Moghaddasi fullname: Moghaddasi, Kiarash organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 3 givenname: Virginia surname: Batignani fullname: Batignani, Virginia organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 4 givenname: Godstime Stephen Kojo surname: Morgan fullname: Morgan, Godstime Stephen Kojo organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 5 givenname: Federico orcidid: 0000-0003-0376-1342 surname: Di Marco fullname: Di Marco, Federico organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 6 givenname: Daniela Maria orcidid: 0000-0001-6415-1535 surname: Cirillo fullname: Cirillo, Daniela Maria organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/39240079$$D View this record in MEDLINE/PubMed |
| BookMark | eNpVkU1PHDEMhiO0CBbKjXOVYw8E8jGfvVUIaKUVXEDqbeVJPNOsZpJpkpG6P7T_h_DRqpUPtmQ_r1_ZJ2TlvENCzgW_FEI2Vzs9XXLeiJLJ4oCsBW8bVlX8--qf-picxLjjXBRFWR6RY9XKgvO6XZPf9-D87AOyDiIamiAMmHIR8eeCTls30IQx0d4HamxAnWhaOgx6GX20kVqDLtneakjWuws6oPNpP2fugoIz1GQ1_dKivqcmLAMNmLkETiOdlvSKxc8UaMxSrNuzl0y1n2YINr5xf105_JVYXoHhlfvfpf7h_OgHi_EDOexhjHj2nk_J0-3N4_VXtnm4-3b9ZcOgEG1iTV1I3paqLivRVdiXwLEG6FQtVSlN00LRAkA-W90JBW2Hvc5RN1hJpQojT8mnN905-Gwkpu1ko8ZxBId-iVsluJCqqiuVRz--jy7dhGY7BztB2G__vEI-A6jlk-s |
| CitedBy_id | crossref_primary_10_1128_jcm_01390_24 crossref_primary_10_1016_j_ijmm_2025_151665 crossref_primary_10_1016_j_ijtb_2025_06_022 crossref_primary_10_1017_ash_2025_10039 crossref_primary_10_1016_j_meegid_2025_105755 crossref_primary_10_1099_acmi_0_001020_v3 crossref_primary_10_1371_journal_pone_0324003 |
| ContentType | Journal Article |
| DBID | CGR CUY CVF ECM EIF NPM 7X8 |
| DOI | 10.1128/jcm.00815-24 |
| DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic |
| DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | no_fulltext_linktorsrc |
| Discipline | Medicine Biology |
| EISSN | 1098-660X |
| ExternalDocumentID | 39240079 |
| Genre | Evaluation Study Journal Article Comparative Study |
| GroupedDBID | --- .55 0R~ 18M 2WC 39C 4.4 53G 5GY 5RE 5VS ABOCM ABPPZ ACGFO ADBBV AENEX AGVNZ ALMA_UNASSIGNED_HOLDINGS AOIJS BAWUL BTFSW CGR CS3 CUY CVF DIK DU5 E3Z EBS ECM EIF F5P FRP GX1 HZ~ KQ8 L7B NPM O9- OK1 P2P P6G RHI RNS RPM RSF TR2 WOQ X7M ZCA ~KM 29K 7X8 AAGFI D-I H13 HYE W8F |
| ID | FETCH-LOGICAL-a419t-874209537561b6ef5a0e7aab372352d89a49aaa0147b13a9befcfcf78e62334d2 |
| IEDL.DBID | 7X8 |
| ISICitedReferencesCount | 7 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=001306440500001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1098-660X |
| IngestDate | Wed Oct 01 17:27:12 EDT 2025 Sat Mar 08 01:25:01 EST 2025 |
| IsDoiOpenAccess | false |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 10 |
| Keywords | rapid tuberculosis laboratory diagnosis respiratory samples targeted next-generation sequencing drug-resistant tuberculosis |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-a419t-874209537561b6ef5a0e7aab372352d89a49aaa0147b13a9befcfcf78e62334d2 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Undefined-3 |
| ORCID | 0009-0001-0144-0759 0000-0001-6415-1535 0000-0001-9727-6465 0000-0003-0376-1342 |
| OpenAccessLink | https://www.ncbi.nlm.nih.gov/pmc/articles/11481573 |
| PMID | 39240079 |
| PQID | 3101236763 |
| PQPubID | 23479 |
| ParticipantIDs | proquest_miscellaneous_3101236763 pubmed_primary_39240079 |
| PublicationCentury | 2000 |
| PublicationDate | 2024-10-16 |
| PublicationDateYYYYMMDD | 2024-10-16 |
| PublicationDate_xml | – month: 10 year: 2024 text: 2024-10-16 day: 16 |
| PublicationDecade | 2020 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | Journal of clinical microbiology |
| PublicationTitleAlternate | J Clin Microbiol |
| PublicationYear | 2024 |
| SSID | ssj0014455 |
| Score | 2.5115268 |
| Snippet | We investigated the performance of the targeted next-generation sequencing (tNGS)-based Oxford Nanopore Diagnostics AmPORE TB assay, recently approved by the... |
| SourceID | proquest pubmed |
| SourceType | Aggregation Database Index Database |
| StartPage | e0081524 |
| SubjectTerms | Antitubercular Agents - pharmacology DNA, Bacterial - genetics Drug Resistance, Bacterial - genetics Genotype Genotyping Techniques - methods High-Throughput Nucleotide Sequencing - methods Humans Molecular Diagnostic Techniques - methods Mutation Mycobacterium tuberculosis - drug effects Mycobacterium tuberculosis - genetics Nanopore Sequencing - methods Nanopores Sputum - microbiology Tuberculosis - diagnosis Tuberculosis - microbiology Tuberculosis, Multidrug-Resistant - diagnosis Tuberculosis, Multidrug-Resistant - microbiology |
| Title | Nanopore-based targeted sequencing test for direct tuberculosis identification, genotyping, and detection of drug resistance mutations: a side-by-side comparison of targeted next-generation sequencing technologies |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/39240079 https://www.proquest.com/docview/3101236763 |
| Volume | 62 |
| WOSCitedRecordID | wos001306440500001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1Nb9QwELWAAuJSoHyVLw0Sx1pNYq8d91JViIoDXfUA0t5WdmxXi2hSNgnS_lD-DzOOtxUHJCQUKcklkZWZzDx7xu8x9j7WwYs4M9zWasalDIE7EyIvXGmaoD2C4MQz-1nP5_ViYc7zgluf2yq3MTEFat81tEZ-KMqJbUyJ46sfnFSjqLqaJTRusx2BUIa8Wi9uqghSJtXTkjgzlSoW28b3qj781lwSs2k547TX_W_gMiWZ04f_O7xHbDfDSziZ_OExuxXaPXZvEpzc7LH7Z7mU_oT9wrjaIfjGr4aJzMPUEo43ubkaUxogDB0AUS1MiQ-G0YV1M37v-lUPK58bjZJtD4DYXocNbb86ANt68GFIbV4tdBH8erwAnNkTWkU3g8txagHoj8ACKYZyt-F0heZaGJGeux5VSzP0i8SRnd75xyhzdQAn_U_Z19OPXz584lnjgVtZmgGDsayI8k4jjnMqxJktgrbWCV0hNPS1sdJYa9GW2pXCGhdig4euA-I2IX31jN1puza8YGAjzrZCoWx0QtZW2LrwplHGK11GDE377N3WdEv8h6gwYtvQjf3yxnj77Plk_-XVRPaxRPxI0vHm5T88_Yo9qBDzUGor1Wu2EzGChDfsbvNzWPXrt8k58Tw_P_sNHIj2Lg |
| linkProvider | ProQuest |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Nanopore-based+targeted+sequencing+test+for+direct+tuberculosis+identification%2C+genotyping%2C+and+detection+of+drug+resistance+mutations%3A+a+side-by-side+comparison+of+targeted+next-generation+sequencing+technologies&rft.jtitle=Journal+of+clinical+microbiology&rft.au=Cabibbe%2C+Andrea+Maurizio&rft.au=Moghaddasi%2C+Kiarash&rft.au=Batignani%2C+Virginia&rft.au=Morgan%2C+Godstime+Stephen+Kojo&rft.date=2024-10-16&rft.issn=1098-660X&rft.eissn=1098-660X&rft.volume=62&rft.issue=10&rft.spage=e0081524&rft_id=info:doi/10.1128%2Fjcm.00815-24&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1098-660X&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1098-660X&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1098-660X&client=summon |