Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

Abstract

Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

Draft Genome Sequences of Two Bison-Type and Two Sheep-Type Strains of Mycobacterium avium subsp. paratuberculosis

“…These lineages are justified by several molecular genotyping methods ( 2 – 5 ). The type C lineage contains a subgroup of type B strains, which have been isolated from both cattle and bison ( 6 , 7 ). Although the type B strains are circulating in Canada and the United States ( 8 , 9 ), they are predominant in Korea ( 7 ) and India ( 10 , 11 ).…”

“…The type C lineage contains a subgroup of type B strains, which have been isolated from both cattle and bison ( 6 , 7 ). Although the type B strains are circulating in Canada and the United States ( 8 , 9 ), they are predominant in Korea ( 7 ) and India ( 10 , 11 ). Type B strains can be distinguished from type C and type S by a novel GTG repeat in the MAP_RS04120 homolog, which encodes MoaD, a molybdenum biosynthesis protein ( 7 ).…”

“…Although the type B strains are circulating in Canada and the United States ( 8 , 9 ), they are predominant in Korea ( 7 ) and India ( 10 , 11 ). Type B strains can be distinguished from type C and type S by a novel GTG repeat in the MAP_RS04120 homolog, which encodes MoaD, a molybdenum biosynthesis protein ( 7 ). The two type B strains sequenced in this study contain 5 GTG repeats typical of type B, while the type S strains contain 3 GTG repeats.…”

Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis

“…Comparative analysis at the genome level has been actively conducted as a strategy to understand the pathogenesis of MAP. Thanks to the recently developed whole genome sequencing technology, additional genome information has become available for many isolates of MAP, and extensive comparative analyses have been performed on functional units of potential virulence factors through pangenome-based analysis [ 14 , 15 ]. Through these studies, it was confirmed that MAP has a highly conserved genome compared to other subspecies, such as M. avium subsp.…”

“…Through these studies, it was confirmed that MAP has a highly conserved genome compared to other subspecies, such as M. avium subsp. hominissuis (Mah), and it shares common virulence genes between MAP strains [ 14 , 15 ]. Comparative genomic analysis at the DNA level has greatly helped in discovering potential virulence factors, but confirmation at the RNA level is necessary to ensure that they actually perform the expected functions in the infectious environment.…”