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A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings
BACKGROUND: In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have eva...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4713439/ https://www.ncbi.nlm.nih.gov/pubmed/26752297 http://dx.doi.org/10.1371/journal.pone.0146106 |
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author | Said, Halima M. Kushner, Nicole Omar, Shaheed V. Dreyer, Andries W. Koornhof, Hendrik Erasmus, Linda Gardee, Yasmin Rukasha, Ivy Shashkina, Elena Beylis, Natalie Kaplan, Gilla Fallows, Dorothy Ismail, Nazir A. |
author_facet | Said, Halima M. Kushner, Nicole Omar, Shaheed V. Dreyer, Andries W. Koornhof, Hendrik Erasmus, Linda Gardee, Yasmin Rukasha, Ivy Shashkina, Elena Beylis, Natalie Kaplan, Gilla Fallows, Dorothy Ismail, Nazir A. |
author_sort | Said, Halima M. |
collection | PubMed |
description | BACKGROUND: In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have evaluated the discriminatory power and clustering concordance of a novel and simple genotyping approach, combining spoligotyping with pncA sequencing (SpoNC), against two well-established methods: IS6110-RFLP and 24-loci MIRU-VNTR. METHODS: A total of 216 MDR-TB isolates collected from January to June 2010 from the NHLS Central TB referral laboratory in Braamfontein, Johannesburg, representing a diversity of strains from South Africa, were included. The isolates were submitted for genotyping, pncA sequencing and analysis to the Centre for Tuberculosis in South Africa and the Public Health Research Institute Tuberculosis Center at Rutgers University in the United States. Clustering rates, Hunter-Gaston Discriminatory Indexes (HGI) and Wallace coefficients were compared between the methods. RESULTS: Overall clustering rates were high by both IS6110-RFLP (52.8%) and MIRU-VNTR (45.8%), indicative of on-going transmission. Both 24-loci MIRU-VNTR and IS6110-RFLP had similar HGI (0.972 and 0.973, respectively), with close numbers of unique profiles (87 vs. 70), clustered isolates (129 vs. 146), and cluster sizes (2 to 26 vs. 2 to 25 isolates). Spoligotyping alone was the least discriminatory (80.1% clustering, HGI 0.903), with 28 unique types. However, the discriminatory power of spoligotyping was improved when combined with pncA sequencing using the SpoNC approach (61.8% clustering, HGI 0.958). A high proportion of MDR-TB isolates had mutations in pncA (68%, n = 145), and pncA mutations were significantly associated with clustering (p = 0.007 and p = 0.0013 by 24-loci MIRU-VNTR and IS6110-RFLP, respectively), suggesting high rates of resistance to pyrazinamide among all MDR-TB cases and particularly among clustered cases. CONCLUSION: We conclude that SpoNC provides good discrimination for MDR-TB surveillance and early identification of outbreaks in South Africa, with 24-loci MIRU-VNTR applied for pncA wild-type strains as needed. |
format | Online Article Text |
id | pubmed-4713439 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-47134392016-01-26 A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings Said, Halima M. Kushner, Nicole Omar, Shaheed V. Dreyer, Andries W. Koornhof, Hendrik Erasmus, Linda Gardee, Yasmin Rukasha, Ivy Shashkina, Elena Beylis, Natalie Kaplan, Gilla Fallows, Dorothy Ismail, Nazir A. PLoS One Research Article BACKGROUND: In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have evaluated the discriminatory power and clustering concordance of a novel and simple genotyping approach, combining spoligotyping with pncA sequencing (SpoNC), against two well-established methods: IS6110-RFLP and 24-loci MIRU-VNTR. METHODS: A total of 216 MDR-TB isolates collected from January to June 2010 from the NHLS Central TB referral laboratory in Braamfontein, Johannesburg, representing a diversity of strains from South Africa, were included. The isolates were submitted for genotyping, pncA sequencing and analysis to the Centre for Tuberculosis in South Africa and the Public Health Research Institute Tuberculosis Center at Rutgers University in the United States. Clustering rates, Hunter-Gaston Discriminatory Indexes (HGI) and Wallace coefficients were compared between the methods. RESULTS: Overall clustering rates were high by both IS6110-RFLP (52.8%) and MIRU-VNTR (45.8%), indicative of on-going transmission. Both 24-loci MIRU-VNTR and IS6110-RFLP had similar HGI (0.972 and 0.973, respectively), with close numbers of unique profiles (87 vs. 70), clustered isolates (129 vs. 146), and cluster sizes (2 to 26 vs. 2 to 25 isolates). Spoligotyping alone was the least discriminatory (80.1% clustering, HGI 0.903), with 28 unique types. However, the discriminatory power of spoligotyping was improved when combined with pncA sequencing using the SpoNC approach (61.8% clustering, HGI 0.958). A high proportion of MDR-TB isolates had mutations in pncA (68%, n = 145), and pncA mutations were significantly associated with clustering (p = 0.007 and p = 0.0013 by 24-loci MIRU-VNTR and IS6110-RFLP, respectively), suggesting high rates of resistance to pyrazinamide among all MDR-TB cases and particularly among clustered cases. CONCLUSION: We conclude that SpoNC provides good discrimination for MDR-TB surveillance and early identification of outbreaks in South Africa, with 24-loci MIRU-VNTR applied for pncA wild-type strains as needed. Public Library of Science 2016-01-11 /pmc/articles/PMC4713439/ /pubmed/26752297 http://dx.doi.org/10.1371/journal.pone.0146106 Text en © 2016 Said et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Said, Halima M. Kushner, Nicole Omar, Shaheed V. Dreyer, Andries W. Koornhof, Hendrik Erasmus, Linda Gardee, Yasmin Rukasha, Ivy Shashkina, Elena Beylis, Natalie Kaplan, Gilla Fallows, Dorothy Ismail, Nazir A. A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings |
title | A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings |
title_full | A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings |
title_fullStr | A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings |
title_full_unstemmed | A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings |
title_short | A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings |
title_sort | novel molecular strategy for surveillance of multidrug resistant tuberculosis in high burden settings |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4713439/ https://www.ncbi.nlm.nih.gov/pubmed/26752297 http://dx.doi.org/10.1371/journal.pone.0146106 |
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