Genome comparison of three serovar 5 pathogenic strains of Haemophilus parasuis: insights into an evolving swine pathogen

Abstract

Haemophilus parasuis is the causative agent of Glä sser's disease, a systemic disorder characterized by polyarthritis, polyserositis and meningitis in pigs. Although it is well known that H. parasuis serovar 5 is the most prevalent serovar associated with the disease, the genetic differences among strains are only now being discovered. Genomes from two serovar 5 strains, SH0165 and 29755, are already available. Here, we present the draft genome of a third H. parasuis serovar 5 strain, the formal serovar 5 reference strain Nagasaki. An in silico genome subtractive analysis with full-length predicted genes of the three H. parasuis serovar 5 strains detected 95, 127 and 95 strain-specific genes (SSGs) for Nagasaki, SH0165 and 29755, respectively. We found that the genomic diversity within these three strains was high, in part because of a high number of mobile elements. Furthermore, a detailed analysis of large sequence polymorphisms (LSPs), encompassing regions ranging from 2 to 16 kb, revealed LSPs in virulence-related elements, such as a Toll-IL receptor, the AcrA multidrug efflux protein, an ATPbinding cassette (ABC) transporter, lipopolysaccharide-synthetizing enzymes and a tripartite ATP-independent periplasmic (TRAP) transporter. The whole-genome codon adaptation index (CAI) was also calculated and revealed values similar to other well-known bacterial pathogens. In addition, whole-genome SNP analysis indicated that nucleotide changes tended to be increased in membrane-related genes. This analysis provides further evidence that the genome of H. parasuis has been subjected to multiple lateral gene transfers (LGTs) and to fine-tuning of virulence factors, and has the potential for accelerated genome evolution.

Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection

“…Additionally, ABC transporters, which have been found to be up-regulated in the current study, have been reported to be essential elements for bacterial survival in the host [ 43 , 44 ]. Interestingly, some ABC transporters could have been acquired via horizontal gene transfer in H. parasuis [ 23 ]. While ABC transporters were found up-regulated, the PTS sugar transport systems were down-regulated, indicating that different sugar transporters could be used depending on the environmental conditions, by opposite regulation of these two ATP-dependent transporters [ 45 ].…”

“…This strain was originally isolated from the meninges of a pig with a systemic infection by H. parasuis in Japan. Gene annotations are based on previous analysis [ 23 ]. Further pathway inspection was performed with Integrated Microbial Genomes (IMG) [ 24 ] and BioCyc [ 25 ].…”

“…RNA-seq analysis was based on the H. parasuis Nagasaki draft genome. The genome is 2.3 Mb in length and was assembled in 47 scaffolds [ 23 ]. The Nagasaki genome encodes 2260 protein-coding genes (with 40 additional putative pseudogenes): 329 annotated as transporters, 754 connected to KEGG pathways and 1418 to KEGG orthology (KO), 1571 are COG annotated and 1918 associated to Pfam.…”

Peer Review #3 of "Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants (v0.1)"

“…and Bello-Orti et al (2014) noted the role of mobile genetic elements and strain-specific accessory genes in fostering high genomic diversity between pathogenic strains of the same serovar from diseased pigs in Japan, China, and the USA.…”

Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica

“…One of the most promising approaches for determining the virulence factors of parasitic organisms is in silico comparison of parasites’ transcripts with publicly available data [ 7 - 10 ]. A recent data resource, the helminth secretome database (HSD) [ 11 , 12 ], contains a broad repertoire of excretory/secretory (ES) protein sequences (n > 18,000) of various parasitic helminths including trematodes, cestodes and nematodes.…”