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J Bacteriol. Feb 2009; 191(4): 1359–1360.
Published online Dec 12, 2008. doi:  10.1128/JB.01682-08
PMCID: PMC2632009

Complete Genome Sequence of Haemophilus parasuis SH0165[down-pointing small open triangle]

Abstract

Haemophilus parasuis is the causative agent of Glässer's disease, which produces big losses in swine populations worldwide. H. parasuis SH0165, belonging to the dominant serovar 5 in China, is a clinically isolated strain with high-level virulence. Here, we report the first completed genome sequence of this species.

Haemophilus parasuis is a commensal organism of the upper respiratory tract of swine that causes severe systemic disease characterized by fibrinous polyserositis, arthritis, and meningitis (11). Fifteen serovars of H. parasuis have been reported, but a high percentage of the evaluated isolates are nontypeable, serovars 4 and 5 are widely associated with epidemics, and serovar 5 is always associated with high-level virulence in pigs (3, 11). Recent progress in H. parasuis research has not elucidated all mechanisms of this species; factors involved in systemic invasion by H. parasuis are still unknown (1, 2, 5, 12). Thus, a highly virulent serovar 5 strain named SH0165, isolated from a Glässer's disease outbreak farm, was chosen for genome sequencing.

The complete genome sequence of H. parasuis SH0165 was determined at the National Human Genome Center at Beijing by using a shotgun sequencing strategy. Draft assemblies were compiled using Consed, based on 20,102 reads, to give sixfold coverage of the genome. Gaps among contigs were closed either by primer walking with selected clones, which were identified by analysis of the forward and reverse links between contigs with the Perl/Tk algorithm, or by sequencing of the DNA amplicons generated by PCR. The genome of H. parasuis strain SH0165 is composed of 2,269,156 bp in a single circular chromosome with an average G+C content of 39.99%, 2,292 predicted coding sequences (CDS), 201 pseudogenes, and 76 structural RNAs. As commonly found for other completed microbial genome sequences, 16.3% of the CDS correspond to hypothetical or conserved hypothetical proteins of unknown functions. Comparative analysis of the draft sequence of H. parasuis 29755, belonging to the same serovar as H. parasuis SH0165, revealed 6.4% unique CDS (143 genes) predicted to be phage genes located in six islands in the SH0165 genome. Thirty-one genes are involved in host and phage regulation and interaction, and there are 11 loci encoding toxin and antitoxin systems, including 9 intact. One prominent feature of the SH0165 genome is that it possesses a large number of transporter-associated genes, accounting for 14.2% of all CDS, which indicates a tremendous ability for environmental adaptation. Though such evidence contradicts the biological traits of H. parasuis, it may point to an evolutionary ancestor of H. parasuis. Another feature of the SH0165 genome is the number of pseudogenes, occurring in about 9.0% of the CDS. This characteristic indicates dramatic evolutionary alteration of the SH0165 genome.

There are numerous virulence-associated genes included in the SH0165 genome, such as the typical two-cluster cdtABC toxin loci, which encode cytolethal distending toxin, a bacterial toxin that initiates a eukaryotic cell cycle block at the G2 stage prior to mitosis (14). Gene oapA, which encodes a surface-associated lipoprotein that is responsible for the transparent colony phenotype of H. influenzae, required for efficient colonization of the nasopharynx, may play an important role in H. parasuis initial adherence (13, 15). The SH0165 genome includes intact type IV secretory system loci named pilABCD, and many more genes, e.g., espP, aidA, and sphB, are autotransporter genes. However, many others are defined as pseudogenes; 11 sclB genes encoding triple-helix-repeat-containing collagen, a large adhensin identified in H. ducreyi, are inactive as a result of frameshifting (4). Both the hhdA and hhdB genes, which are associated with hemolysin, are also defined as pseudogenes. Possibly, changes in the H. parasuis lifestyle led to modifications in the utility of some genes and the high proportion of pseudogenes is related both to the dispensability of previously useful genes in the porcine upper respiratory tract and to a population structure that promotes the maintenance of deleterious mutations (6-10). Pseudogenes in the SH0165 genome have been defined according to the method of Lerat and Ochman and need further investigation with an H. parasuis population (7).

This first determination of the complete genome sequence of the swine commensal H. parasuis SH0165 will facilitate research with this strain and provide not only a foundation for molecular evolution studies of the genetic basis for its systemic invasion and lifestyle but also more efficient vaccine and diagnosis methods to establish disease control measures.

Nucleotide sequence accession number.

The complete genome sequence of the H. parasuis has been assigned GenBank accession number CP001321.

Acknowledgments

This work was supported by the 973 Program (grant no. 2006CB504404), the National Natural Science Foundation of China (grant no. 30530590 and 30600025), the 863 Program (grant no. 2006AA10A206 and 2007AA02Z193), National Scientific and Technical Supporting Programs (grant no. 2006BAD06A01 and 2006BAD06A04), and Innovation Teams of Ministry of Education (grant no. IRT0726).

Footnotes

[down-pointing small open triangle]Published ahead of print on 12 December 2008.

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