A novel DNA chromatography method to discriminate Mycobacterium abscessus subspecies and macrolide susceptibility.
ATS/ERS/ESCMID/IDSA guideline
DNA chromatography
Drug susceptibility
Non-tuberculosis mycobacteria
Subspecies discrimination
Whole genome sequencing
Journal
EBioMedicine
ISSN: 2352-3964
Titre abrégé: EBioMedicine
Pays: Netherlands
ID NLM: 101647039
Informations de publication
Date de publication:
Feb 2021
Feb 2021
Historique:
received:
05
11
2020
revised:
28
11
2020
accepted:
11
12
2020
pubmed:
16
1
2021
medline:
14
10
2021
entrez:
15
1
2021
Statut:
ppublish
Résumé
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. 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. 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%. We developed a novel, rapid and simple DNA chromatography method for identification of MABC macrolide susceptibility with high accuracy. AMED, JSPS KAKENHI.
Sections du résumé
BACKGROUND
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
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
RESULTS
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
CONCLUSIONS
We developed a novel, rapid and simple DNA chromatography method for identification of MABC macrolide susceptibility with high accuracy.
FUNDING
BACKGROUND
AMED, JSPS KAKENHI.
Identifiants
pubmed: 33446475
pii: S2352-3964(20)30563-6
doi: 10.1016/j.ebiom.2020.103187
pmc: PMC7910664
pii:
doi:
Substances chimiques
Anti-Bacterial Agents
0
Macrolides
0
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
103187Informations de copyright
Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Competing Interest Mitsunori Yoshida, Sotaro Sano, Shigehiko Miyamoto and Yoshihiko Hoshino are listed on a pending patent in Japan for the DNA chromatography methodology to distinguish MABC and identify macrolide susceptibility (JP2020–066277 and JP2020–066306). Dr. Morimoto and Dr Kurashima report personal fees as Consultant of INSMED, outside the submitted work. The other authors have nothing to disclose under this manuscript.
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