Kaewprasert Orawee, Nonghanphithak Ditthawat, Chetchotisakd Ploenchan, Namwat Wises, Ong Rick Twee-Hee, Faksri Kiatichai
Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.
Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen 40002, Thailand.
Biology (Basel). 2022 Sep 5;11(9):1319. doi: 10.3390/biology11091319.
Mycobacterium abscessus is an important pathogen that can cause serious human diseases and is difficult to treat due to antibiotic resistance. In this study, we analyzed, using whole-genome sequence (WGS) data, M. abscessus strains serially isolated from patients at various time intervals. We undertook genetic diversity analysis between subspecies, mutation-rate estimation and identification of drug-resistant mutations with minimum inhibitory concentration (MIC) analysis. Clonal isolates of M. abscessus:—subsp. abscessus (MAB) and subsp. massiliense (MMAS)—causing persistent infection through time, differed by 0−7 and 0−14 SNPs, respectively, despite being isolated 1 to 659 days apart. Two cases caused by MMAS differed by ≥102 SNPs at 350 days apart and were regarded as examples of reinfection. Isolates collected ≤7 days apart exhibited a high mutation rate (133.83 ± 0.00 SNPs/genome (5 Mb)/year for MMAS and 127.75 SNPs/genome (5 Mb)/year for MAB). Mutation rates declined in a time-dependent manner in both subspecies. Based on isolates collected > 180 days apart, MMAS had a significantly higher average mutation rate than MAB (2.89 ± 1.02 versus 0.82 ± 0.83 SNPs/genome (5 Mb)/year, (p = 0.01), respectively). All well-known drug-resistance mutations were found to be strongly associated with high MIC levels for clarithromycin and ciprofloxacin. No known mutations were identified for strains resistant to linezolid and amikacin. MAB strains in the study were susceptible to amikacin, while most MMAS strains were susceptible to clarithromycin, amikacin and linezolid. No hetero-resistance was found in the strains analyzed. Our study reports the genetic diversity and mutation rate of M. abscessus between the two major subspecies and confirms the drug resistance-associated mutations. Information about drug-resistance and associated mutations can be applied in diagnosis and patient management.
脓肿分枝杆菌是一种重要的病原体，可导致严重的人类疾病，并且由于抗生素耐药性而难以治疗。在本研究中，我们使用全基因组序列（WGS）数据，分析了在不同时间间隔从患者中连续分离出的脓肿分枝杆菌菌株。我们进行了亚种间的遗传多样性分析、突变率估计以及通过最低抑菌浓度（MIC）分析鉴定耐药突变。脓肿分枝杆菌的克隆分离株——脓肿亚种（MAB）和马西利亚亚种（MMAS）——随着时间推移导致持续感染，尽管分离时间相隔1至659天，但分别相差0至7个和0至14个单核苷酸多态性（SNP）。两例由MMAS引起的病例在相隔350天时相差≥102个SNP，被视为再感染的例子。相隔≤7天收集的分离株表现出高突变率（MMAS为133.83 ± 0.00个SNP/基因组（5 Mb）/年，MAB为127.75个SNP/基因组（5 Mb）/年）。两个亚种的突变率均呈时间依赖性下降。基于相隔> 180天收集的分离株，MMAS的平均突变率显著高于MAB（分别为2.89 ± 1.02与0.82 ± 0.83个SNP/基因组（5 Mb）/年，（p = 0.01））。所有已知的耐药突变均与克拉霉素和环丙沙星的高MIC水平密切相关。对于耐利奈唑胺和阿米卡星的菌株，未鉴定出已知突变。本研究中的MAB菌株对阿米卡星敏感，而大多数MMAS菌株对克拉霉素、阿米卡星和利奈唑胺敏感。在所分析的菌株中未发现异质性耐药。我们的研究报告了脓肿分枝杆菌两个主要亚种之间的遗传多样性和突变率，并证实了与耐药相关的突变。有关耐药性和相关突变的信息可应用于诊断和患者管理。
