TY - JOUR
T1 - A novel DNA chromatography method to discriminate Mycobacterium abscessus subspecies and macrolide susceptibility
AU - Yoshida, Mitsunori
AU - Sano, Sotaro
AU - Chien, Jung Yien
AU - Fukano, Hanako
AU - Suzuki, Masato
AU - Asakura, Takanori
AU - Morimoto, Kozo
AU - Murase, Yoshiro
AU - Miyamoto, Shigehiko
AU - Kurashima, Atsuyuki
AU - Hasegawa, Naoki
AU - Hsueh, Po Ren
AU - Mitarai, Satoshi
AU - Ato, Manabu
AU - Hoshino, Yoshihiko
N1 - Funding Information:
This work was supported in part by grants from the Japan Agency for Medical Research and Development/Japan International Cooperation Agency (AMED) to Y.H. (jp19fk0108043, jp19fk0108064, jp19fk0108075, and jp19jm0510004) and to M.A. (jp19fk0108043 and jp19fk0108049); by grants-in-aid from the Japan Society for Fostering Joint International Research (B) to Y.H. and M.Y. (jp19KK0217), for Early-Career Scientists to M.Y. (jp20K17205) and H.F. (jp18K15966), and for Scientific Research (C) to Y.H. (jp18K08312). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The clinical isolates used in this study were sent from the hospitals and universities listed below. We appreciate the work of all of the clinicians at the following institutions who cared for patients infected with these mycobacteria: Hokkaido Social Insurance Hospital, Fukujuji Hospital Japan Anti-Tuberculosis Association (JATA), Saitama Medical University Hospital, National Hospital Organization (NHO) Tokyo Hospital, Showa University Fujigaoka Hospital, Keio University Hospital, National Defense Medical College Hospital, Kyorin University Hospital, Nagaya City University Hospital, NHO Minami-Kyoto Hospital, Kyoto Prefectural University of Medicine Hospital, Osaka City Northern-City Hospital, Osaka Hospital JATA, NHO Kinki-Chuo Chest Medical Center, NHO Matsue Medical Center, Kawasaki Medical School, NHO Higashi-Hiroshima Medical Center, Kyosai-Yoshijima Hospital, Kyushu University Hospital, and NHO Omuta Hospital. Computations were performed in part on the NIG supercomputer at the ROIS National Institute of Genetics. We thank Ms. Maki Okuda, Sayaka Kashiwagi, and Ginko Kaneda for their assistance.
Funding Information:
This work was supported in part by grants from the Japan Agency for Medical Research and Development/Japan International Cooperation Agency (AMED) to Y.H. (jp19fk0108043, jp19fk0108064, jp19fk0108075, and jp19jm0510004) and to M.A. (jp19fk0108043 and jp19fk0108049); by grants-in-aid from the Japan Society for Fostering Joint International Research (B) to Y.H. and M.Y. (jp19KK0217), for Early-Career Scientists to M.Y. (jp20K17205) and H.F. (jp18K15966), and for Scientific Research (C) to Y.H. (jp18K08312). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The clinical isolates used in this study were sent from the hospitals and universities listed below. We appreciate the work of all of the clinicians at the following institutions who cared for patients infected with these mycobacteria: Hokkaido Social Insurance Hospital, Fukujuji Hospital Japan Anti-Tuberculosis Association (JATA), Saitama Medical University Hospital, National Hospital Organization (NHO) Tokyo Hospital, Showa University Fujigaoka Hospital, Keio University Hospital, National Defense Medical College Hospital, Kyorin University Hospital, Nagaya City University Hospital, NHO Minami-Kyoto Hospital, Kyoto Prefectural University of Medicine Hospital, Osaka City Northern-City Hospital, Osaka Hospital JATA, NHO Kinki-Chuo Chest Medical Center, NHO Matsue Medical Center, Kawasaki Medical School, NHO Higashi-Hiroshima Medical Center, Kyosai-Yoshijima Hospital, Kyushu University Hospital, and NHO Omuta Hospital. Computations were performed in part on the NIG supercomputer at the ROIS National Institute of Genetics. We thank Ms. Maki Okuda, Sayaka Kashiwagi, and Ginko Kaneda for their assistance.
Publisher Copyright:
© 2020 The Authors
PY - 2021/2
Y1 - 2021/2
N2 - Background: The clinical impact of infection with Mycobacterium (M.) abscessus complex (MABC), a group of emerging non-tuberculosis mycobacteria (NTM), is increasing. M. abscessus subsp. abscessus/bolletii frequently shows natural resistance to macrolide antibiotics, whereas M. abscessus subsp. massiliense is generally susceptible. Therefore, rapid and accurate discrimination of macrolide-susceptible MABC subgroups is required for effective clinical decisions about macrolide treatments for MABC infection. We aimed to develop a simple and rapid diagnostic that can identify MABC isolates showing macrolide susceptibility. Methods: Whole genome sequencing (WGS) was performed for 148 clinical or environmental MABC isolates from Japan to identify genetic markers that can discriminate three MABC subspecies and the macrolide-susceptible erm(41) T28C sequevar. Using the identified genetic markers, we established PCR based- or DNA chromatography-based assays. Validation testing was performed using MABC isolates from Taiwan. Finding: We identified unique sequence regions that could be used to differentiate the three subspecies. Our WGS-based phylogenetic analysis indicated that M. abscessus carrying the macrolide-susceptible erm(41) T28C sequevar were tightly clustered, and identified 11 genes that were significantly associated with the lineage for use as genetic markers. To detect these genetic markers and the erm(41) locus, we developed a DNA chromatography method that identified three subspecies, the erm(41) T28C sequevar and intact erm(41) for MABC in a single assay within one hour. The agreement rate between the DNA chromatography-based and WGS-based identification was 99·7%. Interpretation: We developed a novel, rapid and simple DNA chromatography method for identification of MABC macrolide susceptibility with high accuracy. Funding: AMED, JSPS KAKENHI
AB - Background: The clinical impact of infection with Mycobacterium (M.) abscessus complex (MABC), a group of emerging non-tuberculosis mycobacteria (NTM), is increasing. M. abscessus subsp. abscessus/bolletii frequently shows natural resistance to macrolide antibiotics, whereas M. abscessus subsp. massiliense is generally susceptible. Therefore, rapid and accurate discrimination of macrolide-susceptible MABC subgroups is required for effective clinical decisions about macrolide treatments for MABC infection. We aimed to develop a simple and rapid diagnostic that can identify MABC isolates showing macrolide susceptibility. Methods: Whole genome sequencing (WGS) was performed for 148 clinical or environmental MABC isolates from Japan to identify genetic markers that can discriminate three MABC subspecies and the macrolide-susceptible erm(41) T28C sequevar. Using the identified genetic markers, we established PCR based- or DNA chromatography-based assays. Validation testing was performed using MABC isolates from Taiwan. Finding: We identified unique sequence regions that could be used to differentiate the three subspecies. Our WGS-based phylogenetic analysis indicated that M. abscessus carrying the macrolide-susceptible erm(41) T28C sequevar were tightly clustered, and identified 11 genes that were significantly associated with the lineage for use as genetic markers. To detect these genetic markers and the erm(41) locus, we developed a DNA chromatography method that identified three subspecies, the erm(41) T28C sequevar and intact erm(41) for MABC in a single assay within one hour. The agreement rate between the DNA chromatography-based and WGS-based identification was 99·7%. Interpretation: We developed a novel, rapid and simple DNA chromatography method for identification of MABC macrolide susceptibility with high accuracy. Funding: AMED, JSPS KAKENHI
KW - ATS/ERS/ESCMID/IDSA guideline
KW - DNA chromatography
KW - Drug susceptibility
KW - Non-tuberculosis mycobacteria
KW - Subspecies discrimination
KW - Whole genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85100106440&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85100106440&partnerID=8YFLogxK
U2 - 10.1016/j.ebiom.2020.103187
DO - 10.1016/j.ebiom.2020.103187
M3 - Article
C2 - 33446475
AN - SCOPUS:85100106440
VL - 64
JO - EBioMedicine
JF - EBioMedicine
SN - 2352-3964
M1 - 103187
ER -