Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study.
Patients with Mycobacterium tuberculosis isolates sharing identical DNA fingerprint patterns can be epidemiologically linked. However, municipal health services in the Netherlands are able to confirm an epidemiological link in only around 23% of the patients with isolates clustered by the convention...
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| Format: | Article |
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Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5884559?pdf=render |
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| author | Rana Jajou Albert de Neeling Rianne van Hunen Gerard de Vries Henrieke Schimmel Arnout Mulder Richard Anthony Wim van der Hoek Dick van Soolingen |
| author_facet | Rana Jajou Albert de Neeling Rianne van Hunen Gerard de Vries Henrieke Schimmel Arnout Mulder Richard Anthony Wim van der Hoek Dick van Soolingen |
| author_sort | Rana Jajou |
| collection | DOAJ |
| description | Patients with Mycobacterium tuberculosis isolates sharing identical DNA fingerprint patterns can be epidemiologically linked. However, municipal health services in the Netherlands are able to confirm an epidemiological link in only around 23% of the patients with isolates clustered by the conventional variable number of tandem repeat (VNTR) genotyping. This research aims to investigate whether whole genome sequencing (WGS) is a more reliable predictor of epidemiological links between tuberculosis patients than VNTR genotyping.VNTR genotyping and WGS were performed in parallel on all Mycobacterium tuberculosis complex isolates received at the Netherlands National Institute for Public Health and the Environment in 2016. Isolates were clustered by VNTR when they shared identical 24-loci VNTR patterns; isolates were assigned to a WGS cluster when the pair-wise genetic distance was ≤ 12 single nucleotide polymorphisms (SNPs). Cluster investigation was performed by municipal health services on all isolates clustered by VNTR in 2016. The proportion of epidemiological links identified among patients clustered by either method was calculated.In total, 535 isolates were genotyped, of which 25% (134/535) were clustered by VNTR and 14% (76/535) by WGS; the concordance between both typing methods was 86%. The proportion of epidemiological links among WGS clustered cases (57%) was twice as common than among VNTR clustered cases (31%).When WGS was applied, the number of clustered isolates was halved, while all epidemiologically linked cases remained clustered. WGS is therefore a more reliable tool to predict epidemiological links between tuberculosis cases than VNTR genotyping and will allow more efficient transmission tracing, as epidemiological investigations based on false clustering can be avoided. |
| first_indexed | 2024-12-13T09:49:13Z |
| format | Article |
| id | doaj.art-feadf78900264763aece06906847221b |
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| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T09:49:13Z |
| publishDate | 2018-01-01 |
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| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-feadf78900264763aece06906847221b2022-12-21T23:51:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01134e019541310.1371/journal.pone.0195413Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study.Rana JajouAlbert de NeelingRianne van HunenGerard de VriesHenrieke SchimmelArnout MulderRichard AnthonyWim van der HoekDick van SoolingenPatients with Mycobacterium tuberculosis isolates sharing identical DNA fingerprint patterns can be epidemiologically linked. However, municipal health services in the Netherlands are able to confirm an epidemiological link in only around 23% of the patients with isolates clustered by the conventional variable number of tandem repeat (VNTR) genotyping. This research aims to investigate whether whole genome sequencing (WGS) is a more reliable predictor of epidemiological links between tuberculosis patients than VNTR genotyping.VNTR genotyping and WGS were performed in parallel on all Mycobacterium tuberculosis complex isolates received at the Netherlands National Institute for Public Health and the Environment in 2016. Isolates were clustered by VNTR when they shared identical 24-loci VNTR patterns; isolates were assigned to a WGS cluster when the pair-wise genetic distance was ≤ 12 single nucleotide polymorphisms (SNPs). Cluster investigation was performed by municipal health services on all isolates clustered by VNTR in 2016. The proportion of epidemiological links identified among patients clustered by either method was calculated.In total, 535 isolates were genotyped, of which 25% (134/535) were clustered by VNTR and 14% (76/535) by WGS; the concordance between both typing methods was 86%. The proportion of epidemiological links among WGS clustered cases (57%) was twice as common than among VNTR clustered cases (31%).When WGS was applied, the number of clustered isolates was halved, while all epidemiologically linked cases remained clustered. WGS is therefore a more reliable tool to predict epidemiological links between tuberculosis cases than VNTR genotyping and will allow more efficient transmission tracing, as epidemiological investigations based on false clustering can be avoided.http://europepmc.org/articles/PMC5884559?pdf=render |
| spellingShingle | Rana Jajou Albert de Neeling Rianne van Hunen Gerard de Vries Henrieke Schimmel Arnout Mulder Richard Anthony Wim van der Hoek Dick van Soolingen Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study. PLoS ONE |
| title | Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study. |
| title_full | Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study. |
| title_fullStr | Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study. |
| title_full_unstemmed | Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study. |
| title_short | Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study. |
| title_sort | epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing a population based study |
| url | http://europepmc.org/articles/PMC5884559?pdf=render |
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