Genome analysis of Mycoplasma synoviae strain MS-H, the most common M. synoviae strain with a worldwide distribution

Abstract

Background: The bacterial pathogen Mycoplasma synoviae can cause subclinical respiratory disease, synovitis, airsacculitis and reproductive tract disease in poultry and is a major cause of economic loss worldwide. The M. synoviae strain MS-H was developed by chemical mutagenesis of an Australian isolate and has been used as a live attenuated vaccine in many countries over the past two decades. As a result it may now be the most prevalent strain of M. synoviae globally. Differentiation of the MS-H vaccine from local field strains is important for epidemiological investigations and is often required for registration of the vaccine.

Results: The complete genomic sequence of the MS-H strain was determined using a combination of Illumina and Nanopore methods and compared to WVU-1853, the M. synoviae type strain isolated in the USA 30 years before the parent strain of MS-H, and MS53, a more recent isolate from Brazil. The vaccine strain genome had a slightly larger number of pseudogenes than the two other strains and contained a unique 55 kb chromosomal inversion partially affecting a putative genomic island. Variations in gene content were also noted, including a deoxyribose-phosphate aldolase (deoC) fragment and an ATP-dependent DNA helicase gene found only in MS-H. Some of these sequences may have been acquired horizontally from other avian mycoplasma species.

Conclusions: MS-H was somewhat more similar to WVU-1853 than to MS53. The genome sequence of MS-H will enable identification of vaccine-specific genetic markers for use as diagnostic and epidemiological tools to better control M. synoviae.

Keywords: Comparative genetic analysis; Complete genome sequencing; Large chromosomal inversion; MS-H vaccine strain; Mycoplasma synoviae; Vaccine-specific genetic markers.

Fig. 1

MAUVE alignment analysis of M. synoviae genomes, using MS-H as a reference. Similarly colored blocks with connecting lines represent homologous regions. A block below the centre line indicates a region that aligned in reverse complement (inverse) orientation

Fig. 2

Comparative structural analysis of the genomic island (GI) in MS-H, WVU-1853 and MS53. The grey boxes with dotted lines indicate genes identified as part of the genomic island. Hatched arrows indicate genes flanking the GI. The inverted region in MS-H relative to MS53 and WVU-1853 is indicated by crossed solid lines. Inserted/deleted sequences are indicated by dashed lines. Genes with a complete predicted CDS are depicted in black; pseudogenes are depicted in white; tRNA genes are depicted in grey. HP: hypothetical protein. The asterisks indicate sequences duplicated elsewhere in the host genome

Fig. 3

a Location of the deoC gene in M. gallisepticum corresponding to the deoC fragment found in MS-H. b Locations of the ATP-dependent DNA helicase genes in MS-H and M. gallinaceum strain B2096 8B. c, d, e Comparison of unique genomic loci identified in Mycoplasma synoviae strains MS-H, WVU-1853 and MS53. The inserted/deleted sequences are indicated by dotted lines. Genes with complete predicted CDSs are depicted in black; pseudogenes are depicted in white. HP: hypothetical protein

Fig. 4

Organisation of the opp operons in MS-H, MS53 and WVU-1853. a Comparison of operon I in strains MS-H, MS53 and WVU-1853; (b) organisation of operon II in all three strains. Solid arrows indicate functional genes, while vertically hatched arrows indicate pseudogenes. Horizontally hatched arrows indicate hypothetical proteins (HP)

Fig. 5

Organisation of the CRISPR/Cas system genes in the 3 M. synoviae genomes. Solid arrows represent genes. Vertically hatched arrows represent pseudogenes. The checked rectangle indicates the CRISPR repeats