Susceptibility Test Methods: Mycobacteria, <i>Nocardia</i>
, and Other Actinomycetes

Woods, Gail L.; Lin, Shou-Yean Grace; Desmond, Edward

doi:10.1128/9781555817381.ch76

Cited by 83 publications

(111 citation statements)

References 130 publications

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“…Using the microdilution method following the recommendations of the Clinical and Laboratory Standards Institute [Clinical and Laboratory Standards Institute (CLSI) of the rapidly growing mycobacteria with microdilution method][26]. The susceptibility results to ciprofloxacin, moxifloxacin and clarithromycin were judged by the established breakpoints from CLSI document (M24-A2-2011).…”

Section: Methodsmentioning

confidence: 99%

Improved subspecies identification in clinicalMycobacterium abscessuscomplex isolates using whole genome sequence

Lin

Sun

Tan

et al. 2020

Preprint

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16 17 18Mycobacterium abscessus complex, which is frequently reported causing a 19 variety of skin and soft tissues diseases in humans, is composed of three subspecies, 20 namely M. abscessus subsp. abscessus, M. abscessus subsp. massiliense and M. 21 abscessus subsp. bolletii. Currently, the differentiation of these three subspecies in 22 clinical isolates still largely depend on single gene identification methods like the 23 genes namely hsp65, 16s with a limited accuracy. This study confirmed the limitations 24 of the single gene based method in the subspecies identification. We performed a 25 comprehensive analysis of MABC genomes in the NCBI database and tried to build 26 an accurate and user-friendly identify method. Here, we describe an improved assay 27 for Mycobacterium abscessus complex fast identification using WGS data, based on 28 the identities of rpoB, erm(41) and rpls. Comprehensive analysis has been performed 29 to compare our software results with the traditional method. The result showed that the 30 method built-in this study could 100% identification the subspecies for the 31 Mycobacterium abscessus complex in the public genome database (893 genomes from 32 NCBI database and 6 clinical isolates from this study). Because this software can be 33 easily integrated into a routine workflow to quickly and precisely provide 34 subspecies-level identification and discrimination MABC different subspecies in 35 clinical isolates by WGS. This assay will facilitate accurate molecular identification of 36 species from the MABC complex in a variety of clinical specimens and diagnostic 37 contexts. 38 from skin infections to pulmonary [1, 2] is a rapidly growing mycobacterium which 66 becomes an emerging pathogen. MABC is notorious not only because it can 67 accelerate inflammatory damage which leading to increased morbidity and mortality, 68 but also because it causes cystic fibrosis (CF) that had become the most lethal and 69 frequent infection. The notorious MABC complex caused diseases were called 70 nightmares in clinical field, not only because M. abscessus is the second most 71 common nontuberculous mycobacterial species associated with lung disease, but 72 also the intrinsic and acquired resistance of Mycobacterium abscessus to commonly 73 used antibiotics limits the chemotherapeutic options for infections caused by these 74 mycobacteria. So the infections caused by MABC especially the multidrug 75resistance strains were very difficult to treat [3][4][5][6][7], and sometimes impossible to treat, 76 even in the developed countries [8, 9]. 77Despite the high genome similarity, the members of the MABC usually have 78 distinct phenotypes in culture, antibiotic resistance pattern, particularly the critical 79 first line antibiotic treatment-clarithromycin [10, 11], and especially cause differing 80 treatment outcomes for patients infected with M. abscessus subsp. abscessus versus 81 M. abscessus subsp. massiliense [12]. Different treatment requirements and outcomes 82 are thought to vary am...

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Section: Methodsmentioning

confidence: 99%

Improved subspecies identification in clinicalMycobacterium abscessuscomplex isolates using whole genome sequence

Lin

Sun

Tan

et al. 2020

Preprint

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“…Antibiotic susceptibility test. Minimum inhibitory concentrations (MICs) of amikacin and clarithromycin were determined by the broth microdilution method and were interpreted according to the Clinical and Laboratory Standards Institute document M24-A2 (13). Briefly, an appropriate volume of the culture was transferred into 3 ml of sterilized saline until the turbidity matched that of a 0.5 McFarland standard.…”

Section: Methodsmentioning

confidence: 99%

PCR amplification of the erm(41) gene can be used to predict the sensitivity of Mycobacterium�abscessus complex strains to clarithromycin

et al. 2019

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A worldwide increase in the Mycobacterium abscessus (M. abscessus) complex has been observed. Therefore, the aim of the present study was to investigate the diversity of the rrl and erm(41) genes, both of which are associated with macrolide sensitivity in the M. abscessus complex. The current study also examined the efficacy of mass spectrometry as an alternative to molecular testing to classify subspecies of the M. abscessus complex. A total of 14 strains of the M. abscessus complex were obtained, and based on conventional analyses using housekeeping genes, 57% were determined to be M. abscessus subsp. abscessus, 43% were M. abscessus subsp. massiliense, and none were identified as M. abscessus subsp. bolletii. However, depending on the strain, it was not always possible to distinguish between the subspecies by mass spectrometry. Consequently, PCR products for the rrl and erm(41) genes were directly sequenced. Overall, 7.1% of the strains were identified to have a rrl mutation, and 92.9% carried a T at position 28 of erm (41). Results presented here suggest that the principal cause of treatment failure for M. abscessus complex infections is inducible macrolide resistance encoded by the erm(41) gene. From a strictly pragmatic standpoint, the phenotypic function of a putative erm(41) gene is the most important piece of information required by clinicians in order to prescribe an effective treatment. Although PCR amplification of erm(41) is not sufficient to differentiate between the M. abscessus complex subspecies, PCR can be easily and efficiently used to predict the sensitivity of members of the M. abscessus complex to clarithromycin. PCR amplification of the erm(41) gene can be used to predict the sensitivity of Mycobacterium abscessus complex strains to clarithromycin

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“…In proportional DST, resistance was expressed as the percentage of colonies that grew on critical concentrations of the drugs according to the guidelines established by the clinical and laboratory standards institute (CLSI) [13]. Interpretation was made according to the usual criteria for resistance, i.e., 1% for all drugs.…”

Section: Proportional Dstmentioning

confidence: 99%

“…Suspensions were then diluted and inoculated into 96-well microtiter plates to achieve a final organism concentration from 1 × 10 5 to 5 × 10 5 CFU/ml. The antimicrobial agent minimum inhibitory concentrations (MICs) were interpreted according to the guidelines established by the CLSI [13]. Serial double dilutions of antimicrobial agents were prepared ranging from 0.06 to 512 mg/L, added to cation-…”

Section: Broth Microdilutionmentioning

confidence: 99%

Emergence of multidrug-resistantMycobacterium simiae: An in vitro study from a regional tuberculosis reference laboratory in Iran

Nasiri

Amini

Nikpor

et al. 2019

Preprint

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IntroductionMycobacterium simiae is an emerging pathogen in Iran and little is known about drug susceptibility patterns of this pathogen.Materials and methodsTwenty five clinical isolates of M. simiae from 80 patients with confirmed NTM pulmonary disease were included in this study. For drug susceptibility testing (DST), proportional and broth microdilution methods were used according to the clinical and laboratory standards institute (CLSI) guideline.ResultsAll clinical isolates of M. simiae were resistant to isoniazid, rifampicin, ethambutol, streptomycin, amikacin, kanamycin, ciprofloxacin and clarithromycin. They also were highly resistant to ofloxacin (80%). Susceptibility to ofloxacin was only noted in the 5 isolates.ConclusionsClinical isolates of M. simiae were multidrug resistant, and had different drug susceptibility patterns than previously published studies. DST results can assist in selecting more appropriate treatment regimens. Newer drugs with proven clinical efficacy correlating with in vitro susceptibility should be substituted with first- and second line anti-TB drug testing.

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Susceptibility Test Methods: Mycobacteria, Nocardia , and Other Actinomycetes

Cited by 83 publications

References 130 publications

Improved subspecies identification in clinicalMycobacterium abscessuscomplex isolates using whole genome sequence

Improved subspecies identification in clinicalMycobacterium abscessuscomplex isolates using whole genome sequence

PCR amplification of the erm(41) gene can be used to predict the sensitivity of Mycobacterium�abscessus complex strains to clarithromycin

Emergence of multidrug-resistantMycobacterium simiae: An in vitro study from a regional tuberculosis reference laboratory in Iran

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