Evaluation of pyrosequencing for extensive drug resistance-defining anti-tuberculosis drugs for use in public healthcare
MGIT 960 drug susceptibility testing (DST) for Mycobacterium tuberculosis was compared for performance and speed with pyrosequencing (PSQ). Pulmonary samples (n = 100), from GeneXpert/MTB/Rifampicin-resistant patients receiving second-line treatment for 1–3 months, were subjected to DST and PSQ for...
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| Veröffentlicht in: | Tuberculosis (Edinburgh, Scotland) Scotland), 2018-05, Vol.110, p.86-90 |
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| creator | Nambiar, Remya Shah, Daksha Ajbani, Kanchan Kazi, Mubin Sadani, Meeta Shetty, Anjali Keskar, Padmaja Kamble, Sanjeev van Belkum, Alex Rodrigues, Camilla |
| description | MGIT 960 drug susceptibility testing (DST) for Mycobacterium tuberculosis was compared for performance and speed with pyrosequencing (PSQ). Pulmonary samples (n = 100), from GeneXpert/MTB/Rifampicin-resistant patients receiving second-line treatment for 1–3 months, were subjected to DST and PSQ for seven drugs (isoniazid, rifampicin, kanamycin, amikacin, capreomycin, moxifloxacin, and ofloxacin). The mean time-to-result was 35 and two days for DST and PSQ, respectively. Average concordancy was 92.7%. Theoretically, PSQ showed substantial incremental value over the commercial Genotype MTBDRplus/sl. Mutations not considered in commercial molecular tests were observed by PSQ. Our findings corroborated the association between S315T (katG region) and S531L (rpoB region) and phenotypic resistance. PSQ is more rapid, can be performed from the sample, provides information about all known mutations simultaneously, allows extensive post-processing analyses, and is open to the inclusion of new mutations. It indicates the exact mutation conferring resistance to the particular drug, unlike the qualitative DST. |
| doi_str_mv | 10.1016/j.tube.2018.03.006 |
| format | Article |
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Pulmonary samples (n = 100), from GeneXpert/MTB/Rifampicin-resistant patients receiving second-line treatment for 1–3 months, were subjected to DST and PSQ for seven drugs (isoniazid, rifampicin, kanamycin, amikacin, capreomycin, moxifloxacin, and ofloxacin). The mean time-to-result was 35 and two days for DST and PSQ, respectively. Average concordancy was 92.7%. Theoretically, PSQ showed substantial incremental value over the commercial Genotype MTBDRplus/sl. Mutations not considered in commercial molecular tests were observed by PSQ. Our findings corroborated the association between S315T (katG region) and S531L (rpoB region) and phenotypic resistance. PSQ is more rapid, can be performed from the sample, provides information about all known mutations simultaneously, allows extensive post-processing analyses, and is open to the inclusion of new mutations. 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All rights reserved.</rights><rights>Copyright Elsevier Science Ltd. May 2018</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c384t-87861fcf0777a8f12a7a70b13231276d373837469caca4529affe24255d0777c3</citedby><cites>FETCH-LOGICAL-c384t-87861fcf0777a8f12a7a70b13231276d373837469caca4529affe24255d0777c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.tube.2018.03.006$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>315,781,785,3551,27928,27929,45999</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29779779$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nambiar, Remya</creatorcontrib><creatorcontrib>Shah, Daksha</creatorcontrib><creatorcontrib>Ajbani, Kanchan</creatorcontrib><creatorcontrib>Kazi, Mubin</creatorcontrib><creatorcontrib>Sadani, Meeta</creatorcontrib><creatorcontrib>Shetty, Anjali</creatorcontrib><creatorcontrib>Keskar, Padmaja</creatorcontrib><creatorcontrib>Kamble, Sanjeev</creatorcontrib><creatorcontrib>van Belkum, Alex</creatorcontrib><creatorcontrib>Rodrigues, Camilla</creatorcontrib><title>Evaluation of pyrosequencing for extensive drug resistance-defining anti-tuberculosis drugs for use in public healthcare</title><title>Tuberculosis (Edinburgh, Scotland)</title><addtitle>Tuberculosis (Edinb)</addtitle><description>MGIT 960 drug susceptibility testing (DST) for Mycobacterium tuberculosis was compared for performance and speed with pyrosequencing (PSQ). 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It indicates the exact mutation conferring resistance to the particular drug, unlike the qualitative DST.</description><subject>Amikacin</subject><subject>Antitubercular Agents - pharmacology</subject><subject>Bacteria</subject><subject>Capreomycin</subject><subject>DNA, Bacterial - genetics</subject><subject>Drug resistance</subject><subject>Drug Resistance, Multiple, Bacterial - genetics</subject><subject>Drugs</subject><subject>Extensively Drug-Resistant Tuberculosis - microbiology</subject><subject>Feasibility Studies</subject><subject>Genotype</subject><subject>Genotypes</subject><subject>Health care</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humans</subject><subject>Isoniazid</subject><subject>Kanamycin</subject><subject>Microbial Sensitivity Tests - methods</subject><subject>Moxifloxacin</subject><subject>Mutation</subject><subject>Mycobacterium tuberculosis - drug effects</subject><subject>Mycobacterium tuberculosis - genetics</subject><subject>Ofloxacin</subject><subject>Phenotype</subject><subject>Phenotypic DST</subject><subject>Post-production processing</subject><subject>Public Health</subject><subject>Pyrosequencing</subject><subject>Resistance</subject><subject>Rifampin</subject><subject>RpoB protein</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Tuberculosis</subject><issn>1472-9792</issn><issn>1873-281X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kUuLFDEUhYMozjj6B1xIwI2bKpOb6koK3MgwPmDAjYK7kE7dzKSpTto8mpl_b2p6dOFCCCSQ75zcnEPIa856zvj4fteXusUeGFc9Ez1j4xNyzpUUHSj-82k7DxK6SU5wRl7kvGNNxBR7Ts5gknJd5-Tu6miWaoqPgUZHD_cpZvxVMVgfbqiLieJdwZD9Eemc6g1NmH0uJljsZnQ-rJgJxXfrLMnWJbb7BzQ_yGtG6gM91O3iLb1Fs5RbaxK-JM-cWTK-etwvyI9PV98vv3TX3z5_vfx43VmhhtIpqUburGNSSqMcByONZFsuQHCQ4yykUEIO42SNNcMGJuMcwgCbzbxKrLgg706-hxTbv3LRe58tLosJGGvWwAaA9hRsGvr2H3QXawptukYpoRgDPjYKTpRtUeWETh-S35t0rznTay96p9cs9NqLZkK3XprozaN13e5x_iv5U0QDPpwAbFkcPSadrW8t4OwT2qLn6P_n_xt8lqAf</recordid><startdate>201805</startdate><enddate>201805</enddate><creator>Nambiar, Remya</creator><creator>Shah, Daksha</creator><creator>Ajbani, Kanchan</creator><creator>Kazi, Mubin</creator><creator>Sadani, Meeta</creator><creator>Shetty, Anjali</creator><creator>Keskar, Padmaja</creator><creator>Kamble, Sanjeev</creator><creator>van Belkum, Alex</creator><creator>Rodrigues, Camilla</creator><general>Elsevier Ltd</general><general>Elsevier Science Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>C1K</scope><scope>7X8</scope></search><sort><creationdate>201805</creationdate><title>Evaluation of pyrosequencing for extensive drug resistance-defining anti-tuberculosis drugs for use in public healthcare</title><author>Nambiar, Remya ; Shah, Daksha ; Ajbani, Kanchan ; Kazi, Mubin ; Sadani, Meeta ; Shetty, Anjali ; Keskar, Padmaja ; Kamble, Sanjeev ; van Belkum, Alex ; Rodrigues, Camilla</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c384t-87861fcf0777a8f12a7a70b13231276d373837469caca4529affe24255d0777c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Amikacin</topic><topic>Antitubercular Agents - pharmacology</topic><topic>Bacteria</topic><topic>Capreomycin</topic><topic>DNA, Bacterial - genetics</topic><topic>Drug resistance</topic><topic>Drug Resistance, Multiple, Bacterial - genetics</topic><topic>Drugs</topic><topic>Extensively Drug-Resistant Tuberculosis - microbiology</topic><topic>Feasibility Studies</topic><topic>Genotype</topic><topic>Genotypes</topic><topic>Health care</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Humans</topic><topic>Isoniazid</topic><topic>Kanamycin</topic><topic>Microbial Sensitivity Tests - methods</topic><topic>Moxifloxacin</topic><topic>Mutation</topic><topic>Mycobacterium tuberculosis - drug effects</topic><topic>Mycobacterium tuberculosis - genetics</topic><topic>Ofloxacin</topic><topic>Phenotype</topic><topic>Phenotypic DST</topic><topic>Post-production processing</topic><topic>Public Health</topic><topic>Pyrosequencing</topic><topic>Resistance</topic><topic>Rifampin</topic><topic>RpoB protein</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Tuberculosis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nambiar, Remya</creatorcontrib><creatorcontrib>Shah, Daksha</creatorcontrib><creatorcontrib>Ajbani, Kanchan</creatorcontrib><creatorcontrib>Kazi, Mubin</creatorcontrib><creatorcontrib>Sadani, Meeta</creatorcontrib><creatorcontrib>Shetty, Anjali</creatorcontrib><creatorcontrib>Keskar, Padmaja</creatorcontrib><creatorcontrib>Kamble, Sanjeev</creatorcontrib><creatorcontrib>van Belkum, Alex</creatorcontrib><creatorcontrib>Rodrigues, Camilla</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><jtitle>Tuberculosis (Edinburgh, Scotland)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nambiar, Remya</au><au>Shah, Daksha</au><au>Ajbani, Kanchan</au><au>Kazi, Mubin</au><au>Sadani, Meeta</au><au>Shetty, Anjali</au><au>Keskar, Padmaja</au><au>Kamble, Sanjeev</au><au>van Belkum, Alex</au><au>Rodrigues, Camilla</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evaluation of pyrosequencing for extensive drug resistance-defining anti-tuberculosis drugs for use in public healthcare</atitle><jtitle>Tuberculosis (Edinburgh, Scotland)</jtitle><addtitle>Tuberculosis (Edinb)</addtitle><date>2018-05</date><risdate>2018</risdate><volume>110</volume><spage>86</spage><epage>90</epage><pages>86-90</pages><issn>1472-9792</issn><eissn>1873-281X</eissn><abstract>MGIT 960 drug susceptibility testing (DST) for Mycobacterium tuberculosis was compared for performance and speed with pyrosequencing (PSQ). Pulmonary samples (n = 100), from GeneXpert/MTB/Rifampicin-resistant patients receiving second-line treatment for 1–3 months, were subjected to DST and PSQ for seven drugs (isoniazid, rifampicin, kanamycin, amikacin, capreomycin, moxifloxacin, and ofloxacin). The mean time-to-result was 35 and two days for DST and PSQ, respectively. Average concordancy was 92.7%. Theoretically, PSQ showed substantial incremental value over the commercial Genotype MTBDRplus/sl. Mutations not considered in commercial molecular tests were observed by PSQ. Our findings corroborated the association between S315T (katG region) and S531L (rpoB region) and phenotypic resistance. PSQ is more rapid, can be performed from the sample, provides information about all known mutations simultaneously, allows extensive post-processing analyses, and is open to the inclusion of new mutations. It indicates the exact mutation conferring resistance to the particular drug, unlike the qualitative DST.</abstract><cop>Scotland</cop><pub>Elsevier Ltd</pub><pmid>29779779</pmid><doi>10.1016/j.tube.2018.03.006</doi><tpages>5</tpages></addata></record> |
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| ispartof | Tuberculosis (Edinburgh, Scotland), 2018-05, Vol.110, p.86-90 |
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| subjects | Amikacin Antitubercular Agents - pharmacology Bacteria Capreomycin DNA, Bacterial - genetics Drug resistance Drug Resistance, Multiple, Bacterial - genetics Drugs Extensively Drug-Resistant Tuberculosis - microbiology Feasibility Studies Genotype Genotypes Health care High-Throughput Nucleotide Sequencing - methods Humans Isoniazid Kanamycin Microbial Sensitivity Tests - methods Moxifloxacin Mutation Mycobacterium tuberculosis - drug effects Mycobacterium tuberculosis - genetics Ofloxacin Phenotype Phenotypic DST Post-production processing Public Health Pyrosequencing Resistance Rifampin RpoB protein Sequence Analysis, DNA - methods Tuberculosis |
| title | Evaluation of pyrosequencing for extensive drug resistance-defining anti-tuberculosis drugs for use in public healthcare |
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