Chen Kaisen, Zhang Yangyi, Peng Yiping
the First Affiliated Hospital of Nanchang University, Nanchang, China.
J Infect Dev Ctries. 2017 Feb 28;11(2):158-165. doi: 10.3855/jidc.7669.
Characterizing Mycobacterium intracellulare responsible for nontuberculous mycobacterial (NTM) infections may aid in controlling outbreaks. This study aimed to compare 16S ribosomal ribonucleic acid (rRNA) sequencing and variable-number tandem repeat (VNTR) genotyping of M. intracellulare strains isolated from clinical samples, and to characterize VNTR clusters associated with NTM infections or cavity formation.
Sputum samples were obtained from 77 HIV-negative patients with pulmonary disease between 2009 and 2013. One M. intracellulare strain was isolated from each patient and genotyped using 16S rRNA and eight loci VNTR sequencing.
Single nucleotide polymorphism (SNP) genotyping identified seven point mutations at nucleotide positions 101, 178, 190, 252, 382, 443, and 490 in 16S rRNA, and four SNP patterns were identified: type 1 (16 strains), 2 (41 strains), 3 (11 strains), and 4 (1 strain); 5 strains had unique SNP patterns. VNTR genotyping identified VNTR12 as the most discriminating marker (allelic diversity 0.692). VNTR3 was the most homogeneous marker (allelic diversity 0.518), but each locus had high discriminating ability. The 77 strains were clustered according to the unpaired group method using arithmetic averages: cluster 1 (17 strains), 2 (43 strains), 3 (9 strains), and 4 (4 strains); 4strains had unique SNP patterns. Overall, over 90% strains were matched to similar SNP and VNTR groupings. VNTR clusters were associated with NTM infection (p =0.007) and presence of a cavity (p =0.042). Both methods distinguished four subtypes of M. intracellulare, which corresponded.
VNTRs may represent an effective, user-friendly, low-cost typing technique.
鉴定导致非结核分枝杆菌（NTM）感染的胞内分枝杆菌有助于控制疫情暴发。本研究旨在比较从临床样本中分离出的胞内分枝杆菌菌株的16S核糖体核糖核酸（rRNA）测序和可变数目串联重复序列（VNTR）基因分型，并鉴定与NTM感染或空洞形成相关的VNTR簇。
2009年至2013年间，从77例肺部疾病的HIV阴性患者中获取痰液样本。从每位患者中分离出一株胞内分枝杆菌，并使用16S rRNA和8个位点的VNTR测序进行基因分型。
单核苷酸多态性（SNP）基因分型在16S rRNA的核苷酸位置101、178、190、252、382、443和490处鉴定出7个点突变，并鉴定出4种SNP模式：1型（16株）、2型（41株）、3型（11株）和4型（1株）；5株具有独特的SNP模式。VNTR基因分型确定VNTR12是最具鉴别力的标记（等位基因多样性为0.692）。VNTR3是最均匀的标记（等位基因多样性为0.518），但每个位点都具有较高的鉴别能力。使用算术平均值的非配对组方法将77株菌株聚类：1簇（17株）、2簇（43株）、3簇（9株）和4簇（4株）；4株具有独特的SNP模式。总体而言，超过90%的菌株与相似的SNP和VNTR分组相匹配。VNTR簇与NTM感染（p =0.007）和空洞的存在（p =0.042）相关。两种方法都区分了胞内分枝杆菌的4个亚型，它们相互对应。
VNTR可能是一种有效、用户友好、低成本的分型技术。
