Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences

Bannantine, John P.; Condé, Cyril; Bayles, Darrell O.; Branger, Maxime; Biet, Franck

doi:10.3389/fmicb.2020.01701

Cited by 22 publications

(52 citation statements)

References 68 publications

(99 reference statements)

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“…The mosaic nature of MAP based on MAP-S/type III compared with MAP-C genomes but without MAP-S/type I has been described previously [ 34 ], and is especially evident in non-MAP members analyzed elsewhere [ 35 , 74 ]. In contrast to the mosaic structure of different MAP type and subtype genomes presented here, when we compared C type MAP, the same strong synteny of genome structure was observed among MAP-C type strains as previously published [ 34 , 35 ].…”

Section: Resultsmentioning

confidence: 69%

“…Furthermore, there were two large putative rearrangements detected in S397 at 350 kb as well as between 1.4 and 1.5 Mb in the plot (contigs AFIF01000045.1 and AFIF01000121.1 of S397). In addition [ 35 ], a strong synteny was found among the five included MAP-C strains of different origin: K-10, JII-1961, MAP4, E1, and TN/India/2008 ( Figure S1 ), where only one large and two very small rearrangements were identified. These results demonstrate a definite but small amount of genome flexibility among members of MAP-S/type III group and even less flexibility among members of the MAP-C group.…”

Section: Resultsmentioning

confidence: 99%

“…The general higher number of non-synonymous relative to synonymous SNPs (dN/dS ratio) in MAP was discussed before as an indication for ongoing adaptive evolutionary processes possibly to different hosts or environments acting on protein coding genes, and likely reflects the relatively short evolutionary age of MAP [ 75 , 76 ]. Furthermore, a substantially lower dN/dS ratio was identified in 14 MAH and two MAA genomes and was suggested to be associated with a stabilizing selective pressure in these strains [ 35 ]. Obligate Mycobacterium tuberculosis complex pathogens also have a higher dN/dS ratio [ 77 ].…”

Section: Resultsmentioning

confidence: 99%

“…Results of a very recently published comprehensive pan genome and phylogenetic analysis of 28 MAP and non-MAP genomes (including MAH and MAA strains) support the prediction that the core genome evolves through SNPs and recombination events while the accessory genome is acquired by horizontal gene transfer [ 35 ]. In contrast to the non-MAP strains, the included MAP-C genomes were very stable with a low number of SNPs and accessory genes, and a lack of rearrangements [ 35 ].…”

Section: Introductionmentioning

confidence: 83%

“…Another study [ 34 ] challenged the suggestion that M. intracellulare was an ancestor of proto-MAP and explored how well new genomic evidence fit with the previous alternative hypotheses suggesting either evolutionary division of proto-MAP into MAP-S and MAP-C or a successive evolution from such a clone via MAP-S to MAP-C. Currently there is no clear evidence that an ancient MAH subspecies was a progenitor of MAP [ 35 ].…”

Section: Introductionmentioning

confidence: 99%

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Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes

et al. 2020

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Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) is a worldwide-distributed obligate pathogen in ruminants causing Johne’s disease. Due to a lack of complete subtype III genome sequences, there is not yet conclusive information about genetic differences between strains of cattle (MAP-C, type II) and sheep (MAP-S) type, and especially between MAP-S subtypes I, and III. Here we present the complete, circular genome of MAP-S/type III strain JIII-386 (DE) closed by Nanopore-technology and its comparison with MAP-S/type I closed genome of strain Telford (AUS), MAP-S/type III draft genome of strain S397 (U.S.), twelve closed MAP-C strains, and eight closed M.-a.-complex-strains. Structural comparative alignments revealed clearly the mosaic nature of MAP, emphasized differences between the subtypes and the higher diversity of MAP-S genomes. The comparison of various genomic elements including transposases and genomic islands provide new insights in MAP genomics. MAP type specific phenotypic features may be attributed to genes of known large sequence polymorphisms (LSPSs) regions I–IV and deletions #1 and #2, confirmed here, but could also result from identified frameshifts or interruptions of various virulence-associated genes (e.g., mbtC in MAP-S). Comprehensive core and pan genome analysis uncovered unique genes (e.g., cytochromes) and genes probably acquired by horizontal gene transfer in different MAP-types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M.-a.-strains.

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Section: Resultsmentioning

confidence: 69%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 83%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes

et al. 2020

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Mycobacterium : Laboratory Characteristics of Slowly Growing Mycobacteria Other than Mycobacterium tuberculosis

Caulfield,

Richter,

Brown‐Elliott

et al. 2023

ClinMicroNow

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This chapter describes the clinically significant, slowly growing nontuberculous mycobacteria (SGM). Pulsed‐Field Gel Electrophoresis has been a useful technique for strain typing of the SGM. It is important to recognize that an unidentified mycobacterial isolate should be treated as if it is M. tuberculosis and that appropriate safety measures, including biosafety level 3 practices and facilities, should be used until M. tuberculosis is ruled out. One of the first, easiest, and least expensive means of detecting the presence of mycobacteria in clinical samples is microscopic examination. Matrix‐assisted laser desorption ionization‐time‐of‐flight mass spectrometry has revolutionized the identification of microorganisms, including mycobacteria. Not all laboratories may have the necessary funds, facilities, or instrumentation to provide molecular testing in mycobacteriology. Antimicrobial susceptibility testing of clinically relevant mycobacteria is important for the treatment of infections caused by many mycobacterial species.

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Development of a Spectral Library for the Discovery of Altered Genomic Events in Mycobacterium avium Associated With Virulence Using Mass Spectrometry–Based Proteogenomic Analysis

Kotimoole¹,

Antil²,

Kasaragod³

et al. 2023

Molecular & Cellular Proteomics

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Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences

Cited by 22 publications

References 68 publications

Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes

Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes

Mycobacterium : Laboratory Characteristics of Slowly Growing Mycobacteria Other than Mycobacterium tuberculosis

Development of a Spectral Library for the Discovery of Altered Genomic Events in Mycobacterium avium Associated With Virulence Using Mass Spectrometry–Based Proteogenomic Analysis

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