title: Rapid identification of strains belonging to the Mycobacterium abscessus group through erm(41) gene pyrosequencing.
abstract: Mycobacterium abscessus and Mycobacterium massiliense lung infections have different clarithromycin susceptibilities, making proper identification important; however, standard multi-gene sequencing in clinical laboratories is laborious and time consuming. We developed a pyrosequencing-based method for rapid identification of strains belonging to the M. abscessus group by targeting erm(41). We examined 55 isolates from new pulmonary M. abscessus infections and identified 28 M. abscessus, 25 M. massiliense, and 2 Mycobacterium bolletii isolates. Multi-gene sequencing of 16S rRNA, hsp65, rpoB, and the 16S-23S ITS region was concordant with the results of erm(41) pyrosequencing; thus, the M. abscessus group can be identified by single-nucleotide polymorphisms in erm(41). The method also enables rapid identification of polymorphic, inducible clarithromycin-resistant sequevars (T28 or C28). Pyrosequencing of erm(41) is a rapid, reliable, high-throughput alternative method for identifying and characterizing M. abscessus species. Further testing of a diverse collection of isolates is necessary to demonstrate the discriminatory power of erm(41) sequencing to differentiating species with this highly divergent group.
authors.affiliation: Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan. Electronic address: dustin@kch.hosp.go.jp.
authors.forename: Shiomi
authors.initials: S
authors.lastname: Yoshida
authors.affiliation: Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan.
authors.forename: Kazunari
authors.initials: K
authors.lastname: Tsuyuguchi
authors.affiliation: Internal Medicine, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan.
authors.forename: Katsuhiro
authors.initials: K
authors.lastname: Suzuki
authors.affiliation: Clinical laboratory, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan.
authors.forename: Motohisa
authors.initials: M
authors.lastname: Tomita
authors.affiliation: Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan.
authors.forename: Masaji
authors.initials: M
authors.lastname: Okada
authors.affiliation: QIAGEN K.K., 3-13-1 Kachidoki, Chuo-ku, Tokyo 104-0054, Japan.
authors.forename: Ryoko
authors.initials: R
authors.lastname: Shimada
authors.affiliation: Internal Medicine, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan.
authors.forename: Seiji
authors.initials: S
authors.lastname: Hayashi
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001431:Bacteriological Techniques / Q000379:methods*; D001483:Base Sequence; D018834:Chaperonin 60 / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D009161:Mycobacterium / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012359:tRNA Methyltransferases / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D018834:Chaperonin 60; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S; C074119:heat-shock protein 65, Mycobacterium; D012359:tRNA Methyltransferases; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit
keywords: Erm(41); Identification; Inducible clarithromycin resistance; Mycobacterium abscessus; Pyrosequencing