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Macrolides such as clarithromycin are the recommended first line drugs for treatment of\n                      <jats:italic>M. abscessus<\/jats:italic>\n                      infections. However,\n                      <jats:italic>M. abscessus<\/jats:italic>\n                      has dual mechanisms of resistance to macrolides, making treatment by macrolides difficult. A functional\n                      <jats:italic>erm<\/jats:italic>\n                      (41) gene confers for inducible resistance while acquired mutations on the 23S rRNA\n                      <jats:italic>rrl<\/jats:italic>\n                      gene confer for constitutive resistance.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We have developed a real-time PCR assay to detect both inducible and acquired resistance to clarithromycin, and compared the results to traditional\n                      <jats:italic>erm<\/jats:italic>\n                      (41) and\n                      <jats:italic>rrl<\/jats:italic>\n                      sequencing and phenotypic susceptibility testing using Sensititre\u2122 plates.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Of the total 126\u2009\n                      <jats:italic>M. abscessus<\/jats:italic>\n                      isolates tested, truncated\n                      <jats:italic>erm<\/jats:italic>\n                      (41) was found in 23\/126 (18.3%) of the samples, 27\/126 (21.4%) had a T28C mutation in\n                      <jats:italic>erm<\/jats:italic>\n                      (41), and 2\/126 (1.6%) had an acquired A2058C mutation in\n                      <jats:italic>rrl<\/jats:italic>\n                      . The phenotypic results correlated with the expected sequencing results in 121\/126 samples (96%). Phenotypic testing compared to real-time PCR resolved 2 of these discrepancies by showing the existence of both\n                      <jats:italic>erm<\/jats:italic>\n                      (41) alleles in the isolates that sequencing missed. One culture was found to be mixed with two\n                      <jats:italic>M. abscessus<\/jats:italic>\n                      subsp. as per\n                      <jats:italic>hsp65<\/jats:italic>\n                      sequencing and 2 isolates had discordance between molecular and phenotypic results. It was presumed that 3 isolates showed discrepancy between sequencing and real-time PCR, but one culture was mixed and other 2 detected both alleles by real-time PCR leading to 100% concordance when compared to sequencing.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>In conclusion, real-time PCR is more accurate for detection of both acquired and induced clarithromycin resistance, specifically when mixed genic profiles are present in a sample.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12879-020-05686-0","type":"journal-article","created":{"date-parts":[[2020,12,10]],"date-time":"2020-12-10T14:03:19Z","timestamp":1607608999000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["A real-time PCR assay for rapid identification of inducible and acquired clarithromycin resistance in Mycobacterium abscessus"],"prefix":"10.1186","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6020-9995","authenticated-orcid":false,"given":"Meenu Kaushal","family":"Sharma","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanni","family":"La","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Debra","family":"Janella","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hafid","family":"Soualhine","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,12,10]]},"reference":[{"key":"5686_CR1","doi-asserted-by":"publisher","first-page":"67","DOI":"10.3389\/fmicb.2018.00067","volume":"9","author":"RS Gupta","year":"2018","unstructured":"Gupta RS, Lo B, Son J. 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