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. 2022 Jan 31:12:802133.
doi: 10.3389/fmicb.2021.802133. eCollection 2021.

Highly Discriminative Genotyping of Mycobacterium abscessus Complex Using a Set of Variable Number Tandem Repeats in China

Lihua Huang  1 , Haoran Li  2 , Weicong Ren  2 , Xuxia Zhang  2 , Yuanyuan Shang  2 , Yi Liu  2 , Aimei Liu  1 , Yu Pang  2
Affiliations

Highly Discriminative Genotyping of Mycobacterium abscessus Complex Using a Set of Variable Number Tandem Repeats in China

Lihua Huang et al. Front Microbiol. .

Abstract

In this study, our aims were to comparatively analyze the power of variable number tandem repeat (VNTR) typing to discriminate isolates within subspecies and to identify a potential genetic marker for better molecular typing of Mycobacterium abscessus complex (MABC) strains. A total of 103 clinical MABC isolates were collected from a nationwide cross-sectional study in China. Eighteen VNTR loci were chosen to genotype the MABC isolates. Of the 103 clinical MABC isolates, there were 76 (73.8%) M. abscessus subsp. abscessus (MAA) and 27 (26.2%) M. abscessus subsp. massiliense (MAM) isolates. Among the patients with MAA lung diseases, the percentage of patients older than 45 years (67.1%) was significantly higher than that of patients with MAM lung diseases [33.3%, adjusted odds ratio (aOR) = 0.36, 95% CI = 0.13-0.98, p = 0.046]. Fifteen VNTR loci were designated as being "highly discriminant" in our sample, except for TR109. The total of 103 MABC isolates were fully discriminated into 103 unique patterns by an 18-locus VNTR set [Hunter-Gaston Discriminatory Index (HGDI) = 1.000], of which the inclusion of the top 12 loci yielded a comparative HGDI value (HGDI = 0.9998). Remarkably, the order of the diversity of the VNTR loci showed significant difference between the MAA and MAM isolates. TR137 and TR2, two loci with high diversity indices for the MAA isolates, only yielded poor discriminatory power for the MAM isolates; the allelic diversity (h) values were 0.0000 and 0.2621, respectively. A detailed analysis of TR137 in combination with the other 17 VNTR loci showed that the combination of TR137-TR2 could fully distinguish MAA from MAM isolates. In conclusion, our data revealed that MAA is more prone to affect elderly patients. Additionally, the population structure of the MABC isolates circulating in China has high diversity. The combined use of the TR137 and TR2 loci provides a simple criterion for the precise identification of MABC to the subspecies level.

Keywords: MIRU-VNTR; Mycobacterium abscessus complex; genotyping; polymorphism; subspecies.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Phylogenetic tree of 103 Mycobacterium abscessus complex (MABC) strains based on variable number tandem repeat (VNTR) typing created using the BioNumerics v5.0 (Applied Math) the unweighted pair group method with arithmetic mean (UPGMA).
FIGURE 2
FIGURE 2
Hunter–Gaston Discriminatory Index (HGDI) for each variable number tandem repeat (VNTR) locus stratified to different subspecies showing that the TR137 and TR2 loci exhibited the potential to distinguish subspecies within Mycobacterium abscessus complex (MABC).
FIGURE 3
FIGURE 3
Statistical analysis of Mycobacterium abscessus subsp. abscessus (MAA) and M. abscessus subsp. massiliense (MAM) repeats units at 18 tandem repeat (TR) loci showing that the repeat units of the MAM isolates were less than 3 only at TR137 and TR2 of the 18 TR loci (top). When the strains with TR137 repeat units less than 3 were detected again, only the TR2 locus could completely distinguish MAM from MAA (bottom).
FIGURE 4
FIGURE 4
Decision tree diagram based on tandem variable number tandem repeat (VNTR) showing that TR137 combined with the TR2 locus can distinguish Mycobacterium abscessus subsp. abscessus (MAA) and M. abscessus subsp. massiliense (MAM) in the Mycobacterium abscessus complex (MABC).
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