GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance

Hee Jae Huh; Su Young Kim; Hyang Jin Shim; Dae Hun Kim; In Young Yoo; On Kyun Kang; Chang Seok Ki; So Youn Shin; Byung Woo Jhun; Sung Jae Shin; Charles L. Daley; Won Jung Koh; Nam Yong Lee

doi:10.1128/JCM.00516-19

GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance

Hee Jae Huh, Su Young Kim, Hyang Jin Shim, Dae Hun Kim, In Young Yoo, On Kyun Kang, Chang Seok Ki, So Youn Shin, Byung Woo Jhun, Sung Jae Shin, Charles L. Daley, Won Jung Koh, Nam Yong Lee

Department of Microbiology

Research output: Contribution to journal › Article › peer-review

25 Citations (Scopus)

Abstract

We evaluated the GenoType NTM-DR (NTM-DR) line probe assay for identifying Mycobacterium avium complex (MAC) species and Mycobacterium abscessus subspecies and for determining clarithromycin and amikacin resistance. Thirty-eight reference strains and 145 clinical isolates (58 MAC and 87 M. abscessus isolates), including 54 clarithromycin- and/or amikacin-resistant strains, were involved. The performance of the NTM-DR assay in rapid identification was evaluated by comparison with results of multigene sequence-based typing, whereas performance in rapid detection of clarithromycin and amikacin resistance was evaluated by comparison with sequencing of the erm(41), rrl, and rrs genes and drug susceptibility testing (DST). The accuracies of MAC and M. abscessus (sub)species identification were 92.1% (35/38) and 100% (145/145) for the 38 reference strains and 145 clinical isolates, respectively. Three MAC strains other than M. intracellulare were found to cross-react with the M. intracellulare probe in the assay. Regarding clarithromycin resistance, NTM-DR detected rrl mutations in 52 isolates and yielded 99.3% (144/145) and 98.6% (143/145) concordant results with sequencing and DST, respectively. NTM-DR sensitivity and specificity in the detection of clarithromycin resistance were 96.3% (52/54) and 100% (91/91), respectively. The NTM-DR yielded accurate erm(41) genotype results for all 87 M. abscessus isolates. Regarding amikacin resistance, NTM-DR detected rrs mutations in five isolates and yielded 99.3% (144/145) and 97.9% (142/ 145) concordant results with sequencing and DST, respectively. Our results indicate that the NTM-DR assay is a straightforward and accurate approach for discriminating MAC and M. abscessus (sub)species and for detecting clarithromycin and amikacin resistance mutations and that it is a useful tool in the clinical setting.

Original language	English
Article number	e00516-19
Journal	Journal of Clinical Microbiology
Volume	57
Issue number	8
DOIs	https://doi.org/10.1128/JCM.00516-19
Publication status	Published - 2019

Bibliographical note

Funding Information:
This work was supported by the National Research Foundation of Korea (NRF) funded by the South Korean Government (MSIT) (NRF-2018R1A2A1A05018309). Charles L. Daley has received grants from Insmed, Inc., and has served on Advisory Boards for Insmed Inc., Johnson and Johnson, Spero, and Horizon, which were not associated with the submitted work. Won-Jung Koh has received a consultation fee from Insmed, Inc., for the Insmed Advisory Board Meeting, which was not associated with the submitted work. We have no other conflicts of interest to declare.

Funding Information:
This work was supported by the National Research Foundation of Korea (NRF) funded by the South Korean Government (MSIT) (NRF-2018R1A2A1A05018309).

Publisher Copyright:
Copyright © 2019 American Society for Microbiology. All Rights Reserved.

All Science Journal Classification (ASJC) codes

Microbiology (medical)

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10.1128/JCM.00516-19

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Huh, H. J., Kim, S. Y., Shim, H. J., Kim, D. H., Yoo, I. Y., Kang, O. K., Ki, C. S., Shin, S. Y., Jhun, B. W., Shin, S. J., Daley, C. L., Koh, W. J., & Yong Lee, N. (2019). GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance. Journal of Clinical Microbiology, 57(8), [e00516-19]. https://doi.org/10.1128/JCM.00516-19

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title = "GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance",

abstract = "We evaluated the GenoType NTM-DR (NTM-DR) line probe assay for identifying Mycobacterium avium complex (MAC) species and Mycobacterium abscessus subspecies and for determining clarithromycin and amikacin resistance. Thirty-eight reference strains and 145 clinical isolates (58 MAC and 87 M. abscessus isolates), including 54 clarithromycin- and/or amikacin-resistant strains, were involved. The performance of the NTM-DR assay in rapid identification was evaluated by comparison with results of multigene sequence-based typing, whereas performance in rapid detection of clarithromycin and amikacin resistance was evaluated by comparison with sequencing of the erm(41), rrl, and rrs genes and drug susceptibility testing (DST). The accuracies of MAC and M. abscessus (sub)species identification were 92.1% (35/38) and 100% (145/145) for the 38 reference strains and 145 clinical isolates, respectively. Three MAC strains other than M. intracellulare were found to cross-react with the M. intracellulare probe in the assay. Regarding clarithromycin resistance, NTM-DR detected rrl mutations in 52 isolates and yielded 99.3% (144/145) and 98.6% (143/145) concordant results with sequencing and DST, respectively. NTM-DR sensitivity and specificity in the detection of clarithromycin resistance were 96.3% (52/54) and 100% (91/91), respectively. The NTM-DR yielded accurate erm(41) genotype results for all 87 M. abscessus isolates. Regarding amikacin resistance, NTM-DR detected rrs mutations in five isolates and yielded 99.3% (144/145) and 97.9% (142/ 145) concordant results with sequencing and DST, respectively. Our results indicate that the NTM-DR assay is a straightforward and accurate approach for discriminating MAC and M. abscessus (sub)species and for detecting clarithromycin and amikacin resistance mutations and that it is a useful tool in the clinical setting.",

author = "Huh, {Hee Jae} and Kim, {Su Young} and Shim, {Hyang Jin} and Kim, {Dae Hun} and Yoo, {In Young} and Kang, {On Kyun} and Ki, {Chang Seok} and Shin, {So Youn} and Jhun, {Byung Woo} and Shin, {Sung Jae} and Daley, {Charles L.} and Koh, {Won Jung} and {Yong Lee}, Nam",

note = "Funding Information: This work was supported by the National Research Foundation of Korea (NRF) funded by the South Korean Government (MSIT) (NRF-2018R1A2A1A05018309). Charles L. Daley has received grants from Insmed, Inc., and has served on Advisory Boards for Insmed Inc., Johnson and Johnson, Spero, and Horizon, which were not associated with the submitted work. Won-Jung Koh has received a consultation fee from Insmed, Inc., for the Insmed Advisory Board Meeting, which was not associated with the submitted work. We have no other conflicts of interest to declare. Funding Information: This work was supported by the National Research Foundation of Korea (NRF) funded by the South Korean Government (MSIT) (NRF-2018R1A2A1A05018309). Publisher Copyright: Copyright {\textcopyright} 2019 American Society for Microbiology. All Rights Reserved.",

year = "2019",

doi = "10.1128/JCM.00516-19",

language = "English",

volume = "57",

journal = "Journal of Clinical Microbiology",

issn = "0095-1137",

publisher = "American Society for Microbiology",

number = "8",

}

Huh, HJ, Kim, SY, Shim, HJ, Kim, DH, Yoo, IY, Kang, OK, Ki, CS, Shin, SY, Jhun, BW, Shin, SJ, Daley, CL, Koh, WJ & Yong Lee, N 2019, 'GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance', Journal of Clinical Microbiology, vol. 57, no. 8, e00516-19. https://doi.org/10.1128/JCM.00516-19

GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance. / Huh, Hee Jae; Kim, Su Young; Shim, Hyang Jin et al.

In: Journal of Clinical Microbiology, Vol. 57, No. 8, e00516-19, 2019.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance

AU - Huh, Hee Jae

AU - Kim, Su Young

AU - Shim, Hyang Jin

AU - Kim, Dae Hun

AU - Yoo, In Young

AU - Kang, On Kyun

AU - Ki, Chang Seok

AU - Shin, So Youn

AU - Jhun, Byung Woo

AU - Shin, Sung Jae

AU - Daley, Charles L.

AU - Koh, Won Jung

AU - Yong Lee, Nam

N1 - Funding Information: This work was supported by the National Research Foundation of Korea (NRF) funded by the South Korean Government (MSIT) (NRF-2018R1A2A1A05018309). Charles L. Daley has received grants from Insmed, Inc., and has served on Advisory Boards for Insmed Inc., Johnson and Johnson, Spero, and Horizon, which were not associated with the submitted work. Won-Jung Koh has received a consultation fee from Insmed, Inc., for the Insmed Advisory Board Meeting, which was not associated with the submitted work. We have no other conflicts of interest to declare. Funding Information: This work was supported by the National Research Foundation of Korea (NRF) funded by the South Korean Government (MSIT) (NRF-2018R1A2A1A05018309). Publisher Copyright: Copyright © 2019 American Society for Microbiology. All Rights Reserved.

PY - 2019

Y1 - 2019

N2 - We evaluated the GenoType NTM-DR (NTM-DR) line probe assay for identifying Mycobacterium avium complex (MAC) species and Mycobacterium abscessus subspecies and for determining clarithromycin and amikacin resistance. Thirty-eight reference strains and 145 clinical isolates (58 MAC and 87 M. abscessus isolates), including 54 clarithromycin- and/or amikacin-resistant strains, were involved. The performance of the NTM-DR assay in rapid identification was evaluated by comparison with results of multigene sequence-based typing, whereas performance in rapid detection of clarithromycin and amikacin resistance was evaluated by comparison with sequencing of the erm(41), rrl, and rrs genes and drug susceptibility testing (DST). The accuracies of MAC and M. abscessus (sub)species identification were 92.1% (35/38) and 100% (145/145) for the 38 reference strains and 145 clinical isolates, respectively. Three MAC strains other than M. intracellulare were found to cross-react with the M. intracellulare probe in the assay. Regarding clarithromycin resistance, NTM-DR detected rrl mutations in 52 isolates and yielded 99.3% (144/145) and 98.6% (143/145) concordant results with sequencing and DST, respectively. NTM-DR sensitivity and specificity in the detection of clarithromycin resistance were 96.3% (52/54) and 100% (91/91), respectively. The NTM-DR yielded accurate erm(41) genotype results for all 87 M. abscessus isolates. Regarding amikacin resistance, NTM-DR detected rrs mutations in five isolates and yielded 99.3% (144/145) and 97.9% (142/ 145) concordant results with sequencing and DST, respectively. Our results indicate that the NTM-DR assay is a straightforward and accurate approach for discriminating MAC and M. abscessus (sub)species and for detecting clarithromycin and amikacin resistance mutations and that it is a useful tool in the clinical setting.

AB - We evaluated the GenoType NTM-DR (NTM-DR) line probe assay for identifying Mycobacterium avium complex (MAC) species and Mycobacterium abscessus subspecies and for determining clarithromycin and amikacin resistance. Thirty-eight reference strains and 145 clinical isolates (58 MAC and 87 M. abscessus isolates), including 54 clarithromycin- and/or amikacin-resistant strains, were involved. The performance of the NTM-DR assay in rapid identification was evaluated by comparison with results of multigene sequence-based typing, whereas performance in rapid detection of clarithromycin and amikacin resistance was evaluated by comparison with sequencing of the erm(41), rrl, and rrs genes and drug susceptibility testing (DST). The accuracies of MAC and M. abscessus (sub)species identification were 92.1% (35/38) and 100% (145/145) for the 38 reference strains and 145 clinical isolates, respectively. Three MAC strains other than M. intracellulare were found to cross-react with the M. intracellulare probe in the assay. Regarding clarithromycin resistance, NTM-DR detected rrl mutations in 52 isolates and yielded 99.3% (144/145) and 98.6% (143/145) concordant results with sequencing and DST, respectively. NTM-DR sensitivity and specificity in the detection of clarithromycin resistance were 96.3% (52/54) and 100% (91/91), respectively. The NTM-DR yielded accurate erm(41) genotype results for all 87 M. abscessus isolates. Regarding amikacin resistance, NTM-DR detected rrs mutations in five isolates and yielded 99.3% (144/145) and 97.9% (142/ 145) concordant results with sequencing and DST, respectively. Our results indicate that the NTM-DR assay is a straightforward and accurate approach for discriminating MAC and M. abscessus (sub)species and for detecting clarithromycin and amikacin resistance mutations and that it is a useful tool in the clinical setting.

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GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance

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