Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis

Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis

Abstract Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 r...

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Autores principales: Zofia Bakuła, Anna Brzostek, Paulina Borówka, Anna Żaczek, Izabela Szulc-Kiełbik, Agata Podpora, Paweł Parniewski, Dominik Strapagiel, Jarosław Dziadek, Małgorzata Proboszcz, Jacek Bielecki, Jakko van Ingen, Tomasz Jagielski
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Publicado: Nature Portfolio 2018
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Acceso en línea:https://doaj.org/article/ff41f153f3c144ebab3d8c1f901d6c3e
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spelling oai:doaj.org-article:ff41f153f3c144ebab3d8c1f901d6c3e2021-12-02T15:08:23ZMolecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis10.1038/s41598-018-21562-z2045-2322https://doaj.org/article/ff41f153f3c144ebab3d8c1f901d6c3e2018-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-21562-zhttps://doaj.org/toc/2045-2322Abstract Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston’s discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii.Zofia BakułaAnna BrzostekPaulina BorówkaAnna ŻaczekIzabela Szulc-KiełbikAgata PodporaPaweł ParniewskiDominik StrapagielJarosław DziadekMałgorzata ProboszczJacek BieleckiJakko van IngenTomasz JagielskiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Zofia Bakuła
Anna Brzostek
Paulina Borówka
Anna Żaczek
Izabela Szulc-Kiełbik
Agata Podpora
Paweł Parniewski
Dominik Strapagiel
Jarosław Dziadek
Małgorzata Proboszcz
Jacek Bielecki
Jakko van Ingen
Tomasz Jagielski
Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
description Abstract Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston’s discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii.
format article
author Zofia Bakuła
Anna Brzostek
Paulina Borówka
Anna Żaczek
Izabela Szulc-Kiełbik
Agata Podpora
Paweł Parniewski
Dominik Strapagiel
Jarosław Dziadek
Małgorzata Proboszcz
Jacek Bielecki
Jakko van Ingen
Tomasz Jagielski
author_facet Zofia Bakuła
Anna Brzostek
Paulina Borówka
Anna Żaczek
Izabela Szulc-Kiełbik
Agata Podpora
Paweł Parniewski
Dominik Strapagiel
Jarosław Dziadek
Małgorzata Proboszcz
Jacek Bielecki
Jakko van Ingen
Tomasz Jagielski
author_sort Zofia Bakuła
title Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
title_short Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
title_full Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
title_fullStr Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
title_full_unstemmed Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
title_sort molecular typing of mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
publisher Nature Portfolio
publishDate 2018
url https://doaj.org/article/ff41f153f3c144ebab3d8c1f901d6c3e
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