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Case Reports
. 2017 Jan 31:12:16.
doi: 10.1186/s40793-017-0234-6. eCollection 2017.

Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection

Rafael A Baraúna  1 , Rommel T J Ramos  1 , Adonney A O Veras  1 , Pablo H C G de Sá  1 , Luís C Guimarães  1 , Diego A das Graças  1 , Adriana R Carneiro  1 , Judy M Edman  2 , Sharon J Spier  2 , Vasco Azevedo  3 , Artur Silva  1
Affiliations
Case Reports

Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection

Rafael A Baraúna et al. Stand Genomic Sci. .

Abstract

The genomes of four strains (MB11, MB14, MB30, and MB66) of the species Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, completely assembled, and their gene content and structure were analyzed. The strains were isolated from horses with distinct signs of infection, including ulcerative lymphangitis, external abscesses on the chest, or internal abscesses on the liver, kidneys, and lungs. The average size of the genomes was 2.3 Mbp, with 2169 (Strain MB11) to 2235 (Strain MB14) predicted coding sequences (CDSs). An optical map of the MB11 strain generated using the KpnI restriction enzyme showed that the approach used to assemble the genome was satisfactory, producing good alignment between the sequence observed in vitro and that obtained in silico. In the resulting Neighbor-Joining dendrogram, the C. pseudotuberculosis strains sequenced in this study were clustered into a single clade supported by a high bootstrap value. The structural analysis showed that the genomes of the MB11 and MB14 strains were very similar, while the MB30 and MB66 strains had several inverted regions. The observed genomic characteristics were similar to those described for other strains of the same species, despite the number of inversions found. These genomes will serve as a basis for determining the relationship between the genotype of the pathogen and the type of infection that it causes.

Keywords: Biovar equi; C. pseudotuberculosis; Genomic; Horse; Ulcerative lymphangitis.

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Figures

Fig. 1
Fig. 1
Transmission Electron Micrograph of three strains sequenced in this study. The electron micrographs of a MB11, b MB30 and c MB66, demonstrate the pleomorphic morphology of the species
Fig. 2
Fig. 2
Dendrogram of the representative genomes in the CMNR group. The analysis was performed using MEGA 5.10. Only bootstraps greater than 50% are shown in the branches of the dendrogram. The accession numbers for the sequences used in the analysis are: C. pseudotuberculosis MB11 (CP013260), C. pseudotuberculosis MB14 (CP013261), C. pseudotuberculosis MB30 (CP013262), C. pseudotuberculosis MB66 (CP013263), C. pseudotuberculosis 316 (CP003077), C. pseudotuberculosis 258 (CP003540), C. pseudotuberculosis 1002 (CP001809), C. pseudotuberculosis C231 (CP001829), C. diphtheriae NCTC 13129 (BX248353), C. glutamicum ATCC 13032 (BA000036), C. striatum ATCC 6940 (GCA_000159135), C. accolens ATCC 49725 (GCA_000159115), C. pseudogenitalium ATCC 33035 (NZ_ABYQ00000000), C. jeikeium K411 (NC_007164), N. brasiliensis ATCC 700358 (CP003876), N. farcinica IFM 10152 (NC_006361), M. bovis AF2122/97 (BX248333), M. ulcerans Agy99 (CP000325), M. smegmatis MC2 155 (CP000480), R. equi 103S (FN563149), R. fascians NBRC 12155 (GCA_001894785), R. erythropolis PR4 (NC_012490), R. jostii RHA1 (NC_008268)
Fig. 3
Fig. 3
Optical map of Corynebacterium pseudotuberculosis MB11. The figure shows the alignment of the KpnI sites observed in the optical map (bottom scale bar) with those predicted by the in silico assembly (top scale bar). Vertical lines connect identical restriction sites observed in the optical map and those predicted by the assembly, demonstrating that the genome was assembled in the correct order
Fig. 4
Fig. 4
Circular map of the genome for the sequenced Corynebacterium pseudotuberculosis strains. The outermost ring in blue shows the features extracted from the MB11 genome using a .gbk file. The next ring shows the CDSs predicted on the forward strand of MB11 in red, followed by the CDSs on the reverse strand with their features in blue. The other three rings in red, green, and blue show proteins predicted by blastx for the MB14, MB30, and MB66 genomes, respectively, compared to the MB11 genome. The two innermost rings show the GC content and GC skew, followed by the size of the genome in base pairs
Fig. 5
Fig. 5
Comparison of C. pseudotuberculosis genome structures using blastn. The names of the strains are indicated at the side of the gray bars showing the size of each genome. Red bars show conserved regions between two genomes using an e-value of 1-e05, while blue bars show inverted regions
See this image and copyright information in PMC

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