Role and value of whole genome sequencing in studying tuberculosis transmission
Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. To summarize the eviden...
Uloženo v:
| Vydáno v: | Clinical microbiology and infection Ročník 25; číslo 11; s. 1377 |
|---|---|
| Hlavní autoři: | , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
England
01.11.2019
|
| Témata: | |
| ISSN: | 1469-0691, 1469-0691 |
| On-line přístup: | Zjistit podrobnosti o přístupu |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations.
To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission.
A total of 69 peer-reviewed publications identified in Pubmed database.
Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles.
WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached. |
|---|---|
| AbstractList | Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations.
To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission.
A total of 69 peer-reviewed publications identified in Pubmed database.
Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles.
WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached. Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations.BACKGROUNDTuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations.To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission.OBJECTIVESTo summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission.A total of 69 peer-reviewed publications identified in Pubmed database.SOURCESA total of 69 peer-reviewed publications identified in Pubmed database.Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles.CONTENTEvidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles.WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached.IMPLICATIONSWGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached. |
| Author | van der Werf, M J Tagliani, E Nikolayevskyy, V Niemann, S Anthony, R van Soolingen, D Ködmön, C Cirillo, D M |
| Author_xml | – sequence: 1 givenname: V surname: Nikolayevskyy fullname: Nikolayevskyy, V email: vlad.nikolayevskyy@phe.gov.uk organization: Public Health England, London, UK; Imperial College, London, UK. Electronic address: vlad.nikolayevskyy@phe.gov.uk – sequence: 2 givenname: S surname: Niemann fullname: Niemann, S organization: Molecular and Experimental Mycobacteriology, National Reference Centre for Mycobacteria, Research Centre, Borstel, Germany; German Centre for Infection Research, Borstel site, Germany – sequence: 3 givenname: R surname: Anthony fullname: Anthony, R organization: Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands – sequence: 4 givenname: D surname: van Soolingen fullname: van Soolingen, D organization: Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands – sequence: 5 givenname: E surname: Tagliani fullname: Tagliani, E organization: Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 6 givenname: C surname: Ködmön fullname: Ködmön, C organization: European Centre for Disease Prevention and Control, Stockholm, Sweden – sequence: 7 givenname: M J surname: van der Werf fullname: van der Werf, M J organization: European Centre for Disease Prevention and Control, Stockholm, Sweden – sequence: 8 givenname: D M surname: Cirillo fullname: Cirillo, D M organization: Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30980928$$D View this record in MEDLINE/PubMed |
| BookMark | eNpNUE1Lw0AUXKRiP_QHeJE9eml8-7bZZo9S_IJCQfQcNpu3NSXZrdlE6b83xQqeZhiGYWambOSDJ8auBSQChLrbJbapEgShE5AJIJ6xiVgoPQelxegfH7NpjDsAQCkXF2wsQWegMZuwzWuoiRtf8i9T98SD498fR2lLPjTEI3325G3lt7zyPHZ9eTjyri-otX0dYhV51xofmyrGKvhLdu5MHenqhDP2_vjwtnqerzdPL6v79dzKVHZza7BULlVapS4jQ6U1KabWyIxQCmccObRaEUApLA4LHBVLsJkmqwvpFM7Y7W_uvg1Dw9jlQwFLdW08hT7miKAVLFFng_XmZO2Lhsp831aNaQ_53wn4A_z4YwE |
| CitedBy_id | crossref_primary_10_1016_j_jiph_2023_05_020 crossref_primary_10_1016_j_heliyon_2023_e22898 crossref_primary_10_3389_fpubh_2022_956171 crossref_primary_10_1055_a_1934_8303 crossref_primary_10_1183_13993003_01888_2019 crossref_primary_10_1080_10408363_2020_1720591 crossref_primary_10_1099_mgen_0_000418 crossref_primary_10_1186_s40001_019_0397_2 crossref_primary_10_2147_IDR_S437026 crossref_primary_10_1099_mgen_0_000850 crossref_primary_10_3389_fcimb_2022_887134 crossref_primary_10_1093_femsre_fuaf017 crossref_primary_10_1128_spectrum_00418_24 crossref_primary_10_1590_0037_8682_0013_2022 crossref_primary_10_1016_j_meegid_2021_104861 crossref_primary_10_1186_s12879_020_4832_3 crossref_primary_10_1093_jambio_lxac046 crossref_primary_10_1093_femsre_fuaa071 crossref_primary_10_1016_j_meegid_2023_105508 crossref_primary_10_1016_j_jiac_2025_102795 crossref_primary_10_1016_j_meegid_2019_104107 crossref_primary_10_1183_13993003_01154_2019 crossref_primary_10_7554_eLife_76780 crossref_primary_10_1016_j_meegid_2021_105107 crossref_primary_10_1038_s41598_022_23343_1 crossref_primary_10_1016_j_cmi_2023_10_023 crossref_primary_10_3390_antibiotics14070625 crossref_primary_10_1016_j_tube_2022_102185 crossref_primary_10_1128_spectrum_02244_22 crossref_primary_10_1038_s41598_025_94646_2 crossref_primary_10_3389_fmicb_2021_754352 crossref_primary_10_1371_journal_pone_0319630 crossref_primary_10_46234_ccdcw2025_183 crossref_primary_10_1038_s41598_021_00890_7 crossref_primary_10_3389_fcimb_2024_1488547 crossref_primary_10_1136_bmjopen_2022_066651 crossref_primary_10_3389_fcimb_2021_707244 crossref_primary_10_1128_aac_00430_24 crossref_primary_10_1016_j_micpath_2023_106248 crossref_primary_10_1007_s10096_020_04100_6 crossref_primary_10_3201_eid3008_240021 crossref_primary_10_1093_infdis_jiad515 crossref_primary_10_1080_14737159_2024_2362165 crossref_primary_10_3389_fmicb_2024_1413618 crossref_primary_10_1038_s41598_019_51812_7 crossref_primary_10_1128_spectrum_00310_22 crossref_primary_10_1371_journal_pcbi_1008678 crossref_primary_10_1183_13993003_02272_2020 crossref_primary_10_1016_j_meegid_2023_105484 crossref_primary_10_1093_infdis_jiae240 crossref_primary_10_7554_eLife_76605 crossref_primary_10_1093_cid_ciaa1224 crossref_primary_10_3389_fpubh_2021_790544 |
| ContentType | Journal Article |
| Copyright | Crown Copyright © 2019. Published by Elsevier Ltd. All rights reserved. |
| Copyright_xml | – notice: Crown Copyright © 2019. Published by Elsevier Ltd. All rights reserved. |
| DBID | CGR CUY CVF ECM EIF NPM 7X8 |
| DOI | 10.1016/j.cmi.2019.03.022 |
| 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 | 1469-0691 |
| ExternalDocumentID | 30980928 |
| Genre | Evaluation Study Journal Article Review |
| GroupedDBID | --- --M .3N .GA .Y3 05W 0R~ 10A 1OC 29B 2WC 31~ 36B 4.4 457 50Y 50Z 51W 51X 52M 52N 52O 52P 52R 52S 52T 52W 52X 53G 5GY 5HH 5LA 5VS 66C 6J9 702 7PT 7X7 8-0 8-1 8-3 8-4 8-5 88E 8C1 8FE 8FH 8FI 8FJ 8FQ 8R4 8R5 8UM 930 A01 A03 A8Z AACTN AAEDW AAHHS AAIKJ AALRI AANHP AAONW AAXUO ABCQN ABDBF ABEML ABJNI ABMAC ABOCM ABUWG ACBWZ ACCFJ ACGFO ACGFS ACPRK ACRPL ACSCC ACUHS ACXQS ACYXJ ADBBV ADEZE ADNMO ADVLN ADZOD AEEZP AENEX AEQDE AEUYN AEXQZ AFBPY AFEBI AFETI AFJKZ AFKRA AFRAH AFTJW AFZJQ AGHFR AHEFC AHMBA AITUG AIWBW AJAOE AJBDE AKRWK ALIPV ALMA_UNASSIGNED_HOLDINGS AMRAJ ASPBG AVWKF AZBYB AZFZN BAFTC BAWUL BBNVY BDRZF BENPR BHPHI BPHCQ BVXVI BY8 CAG CCPQU CGR COF CS3 CUY CVF D-6 D-7 D-E D-F DCZOG DIK DR2 DWQXO E3Z EAD EAP EBC EBD EBS ECM EDH EIF EJD EMB EMK EMOBN ESX EX3 F00 F01 F04 F5P FDB FEDTE FYUFA G-S G.N GI5 GODZA H.X HCIFZ HF~ HMCUK HOLLA HVGLF HZI HZ~ IHE IX1 IXB J0M K48 LC2 LC3 LH4 LK8 LP6 LP7 LW6 M1P M3C M3G M41 M7P MK4 MM. N04 N05 N9A NF~ NPM O9- OIG OK1 OVD P2P P2X P2Z P4B P4D PHGZT PQQKQ PROAC PSQYO Q.N Q11 Q2X QB0 R.K ROL RWL RX1 RXW SSZ SUPJJ SV3 TAE TEORI TUS UB1 UKHRP V8K V9Y W8V W99 WOW WQJ WXI WYUIH X6Y XG1 YFH ~IA ~WT 7X8 AAYWO ACVFH ADCNI AEUPX AFPUW AIGII AKBMS AKYEP EFKBS WIN |
| ID | FETCH-LOGICAL-c353t-ca2d6f56965f8eaedca525ca38e231fafef2c96e00d1c2691feb70c89ec9b3f62 |
| IEDL.DBID | 7X8 |
| ISICitedReferencesCount | 61 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000492683600013&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1469-0691 |
| IngestDate | Sun Sep 28 07:26:37 EDT 2025 Thu Apr 03 07:08:01 EDT 2025 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 11 |
| Keywords | Outbreak Tuberculosis Whole genome sequencing Standardization Transmission |
| Language | English |
| License | Crown Copyright © 2019. Published by Elsevier Ltd. All rights reserved. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c353t-ca2d6f56965f8eaedca525ca38e231fafef2c96e00d1c2691feb70c89ec9b3f62 |
| Notes | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 ObjectType-Review-4 content type line 23 |
| PMID | 30980928 |
| PQID | 2209607298 |
| PQPubID | 23479 |
| ParticipantIDs | proquest_miscellaneous_2209607298 pubmed_primary_30980928 |
| PublicationCentury | 2000 |
| PublicationDate | 2019-Nov 20191101 |
| PublicationDateYYYYMMDD | 2019-11-01 |
| PublicationDate_xml | – month: 11 year: 2019 text: 2019-Nov |
| PublicationDecade | 2010 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England |
| PublicationTitle | Clinical microbiology and infection |
| PublicationTitleAlternate | Clin Microbiol Infect |
| PublicationYear | 2019 |
| SSID | ssj0002334 |
| Score | 2.533572 |
| SecondaryResourceType | review_article |
| Snippet | Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium... |
| SourceID | proquest pubmed |
| SourceType | Aggregation Database Index Database |
| StartPage | 1377 |
| SubjectTerms | Disease Transmission, Infectious Humans Molecular Epidemiology - methods Mycobacterium tuberculosis - classification Mycobacterium tuberculosis - genetics Mycobacterium tuberculosis - isolation & purification Sensitivity and Specificity Tuberculosis - transmission Whole Genome Sequencing - methods |
| Title | Role and value of whole genome sequencing in studying tuberculosis transmission |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/30980928 https://www.proquest.com/docview/2209607298 |
| Volume | 25 |
| WOSCitedRecordID | wos000492683600013&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/eLvHCXMwpV1bS8MwFA7qVHzxfpk3IvgabJM2TZ5ExOGDm0NU9jbS5AQKWzvXTfHfm7QdexIEX0pfCuH0JOc7l3wfQtcu3zIhNwmRIgASRSwhikUxUWkEMrARD6pb_O9PSa8nBgPZbwpuZTNWuTgTq4PaFNrXyG8o9WDbQUFxO_kgXjXKd1cbCY1V1GIOyviRrmSwZAunrO4quxSQBFyGi65mNd-lx5mf7Ko5Tr127m8Is4o0nZ3_rnEXbTcYE9_VTrGHViDfRxu16uT3PtrsNv30A_T8UowAq9xgT_oNuLD4ywvmYk_dOgbcDFq78IazHFdUtP59Nk9hquejosxKPPPRznmLL7sdorfOw-v9I2kkFohmMZsRrajhNuaSx1aAAqNVTGOtmAAH_KyyYKmWHILAhJo6E1pIk0ALCVqmzHJ6hNbyIocThLkRoTah5cplYMIYqaPUJkZwFqVcyriNrhZGG7pF-b6EyqGYl8Ol2drouLb8cFJzbQxZ4JxIUnH6h6_P0Jb_ofVNwXPUsm4DwwVa15-zrJxeVr7hnr1-9wfedcRs |
| 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=Role+and+value+of+whole+genome+sequencing+in+studying+tuberculosis+transmission&rft.jtitle=Clinical+microbiology+and+infection&rft.au=Nikolayevskyy%2C+V&rft.au=Niemann%2C+S&rft.au=Anthony%2C+R&rft.au=van+Soolingen%2C+D&rft.date=2019-11-01&rft.eissn=1469-0691&rft.volume=25&rft.issue=11&rft.spage=1377&rft_id=info:doi/10.1016%2Fj.cmi.2019.03.022&rft_id=info%3Apmid%2F30980928&rft_id=info%3Apmid%2F30980928&rft.externalDocID=30980928 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1469-0691&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1469-0691&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1469-0691&client=summon |