Draft Genome Sequence of the Host-Restricted Salmonella enterica Serovar Abortusovis Strain SS44

Abstract

Salmonella enterica serovar Abortusovis is a pathogen strictly adapted to ovines, in which it causes abortion. To enhance our understanding of this pathogen, we assembled the first draft sequence of an S. Abortusovis genome (strain SS44). The obtained genomic data might facilitate the study of S. enterica evolution and host adaptation.

GENOME ANNOUNCEMENT

The ovine pathogen Salmonella enterica serovar Abortusovis is endemic in several European and Asian countries, where it causes significant economic losses due to the high rates of abortion in infected flocks. The introduction of S. Abortusovis epidemic strains in new areas is difficult to control due to the asymptomatic behaviors in infected adult lambs, rams, and nonpregnant ewes (1). Strain SS44 is a clinical isolate (2) that has been widely used to study S. Abortusovis virulence features by means of in vitro assays and animal experimental models (1, 3, 4). The genome sequence was obtained by a whole-genome shotgun strategy using the Roche 454 Life Sciences GS-20 sequencer and GS-FLX sequencer (478,585 reads totaling 51,883,128 bp). Reads from 3 pyrosequencing runs were assembled using the GS de novo Assembler software and GS Reference Mapper software (with published Salmonella genomes). Gaps were closed manually, reaching an assembly of 213 contigs (N₅₀ length, 54,599 bp) corresponding to a total of 4,508,347 bp. The draft genome of SS44 has an estimated size of 4.6 Mb, with a G+C content of 52.1%. Contig annotation performed using the Prodigal version 1.20 analysis server (5) predicted 4,924 coding genes. Of these, 2,884 have a full-length homolog in other genomes of S. enterica strains (BLASTp protein identity, ≥80% for ≥80% protein length; E value, <10^-8). Six contigs (42,800 bp in total) have a high similarity (>90%) with other S. enterica serovar virulence plasmids (GenBank accession no. AE006471, EU219534, AY517905, HE663166, and JN885080).

SS44 carries IS1414, a 1,344-bp insertion sequence (IS) that has been detected in several pathotypes of Escherichia coli infecting both humans and domesticated animals (3, 6). Read alignment with IS1414-borne tnpA gene sequence showed a coverage of ~100×, confirming a high copy number, as was previously suggested (3). As expected, the high number of IS1414 copies affected the ability to automatically assemble the pyrosequencing reads and hampered the labor of gap closures through directed PCR and primer walking approaches. IS1414 might have been recently transferred from E. coli into S. Abortusovis, since strains isolated in Asia do not carry this IS element (3). The adaptation of S. Abortusovis to sheep might also be recent, since high copy numbers of IS elements have been observed in the genomes of bacteria adapted only recently to a host-restricted pathogenic lifestyle (4, 7–10). Six Salmonella pathogenicity islands (SPI-1 to SPI-6) were reported to be present in SS44, with major degradation in SPI-3 and SPI-6 (of about 4 kbp and 20 kbp, respectively). Host-adapted and host-restricted serovars of S. enterica have been reported to depend on their environment for amino acids and essential nutrients (10). The SS44 draft genome shows that S. Abortusovis auxotrophy for cysteine and nicotinic acid is due to mutations in the cysI, nadB, and nadC genes. Further analysis of the SS44 genome will help to understand the S. Abortusovis evolution toward an ovine-restricted pathogenicity.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AUYQ00000000. The version described in this paper is version AUYQ02000000.