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Brachyspira spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity. Brachyspira intermedia can cause production losses in chickens and strain PWS/AT now becomes the fourth genome to be completed in the genus Brachyspira. 15 classes of unique and shared genes were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B. pilosicoli. The largest number of unique genes was found in B. intermedia and B. murdochii. This indicates the presence of larger pan-genomes. In general, hypothetical protein annotations are overrepresented among the unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT. The plasmid was also present in the B. murdochii strain but not in nine other Brachyspira isolates. Within the Brachyspira genomes, genes had been translocated and also frequently switched between leading and lagging strands, a process that can be followed by different AT-skews in the third positions of synonymous codons. We also found evidence that bacteriophages were being remodeled and genes incorporated into them. The accessory gene pool shapes species-specific traits. It is also influenced by reductive genome evolution and horizontal gene transfer. Gene-transfer events can cross both species and genus boundaries and bacteriophages appear to play an important role in this process. A mechanism for horizontal gene transfer appears to be gene translocations leading to remodeling of bacteriophages in combination with broad tropism.

Elbers A.,Wageningen University | Knutsson R.,National Veterinary Institute SVA
Biosecurity and Bioterrorism | Year: 2013

Agroterrorism targeting livestock can be described as the intentional introduction of an animal disease agent against livestock with the purpose of causing economic damage, disrupting socioeconomic stability of a country, and creating panic and distress. This type of terrorism can be alluring to terrorists because animal disease agents are easily available. This review addresses the vulnerabilities of the livestock industry to agroterrorism. However, we also show that early detection systems have recently been developed for agroterrorism and deliberate spread of animal pathogens in livestock, including an agroterrorism intelligence cycle, syndromic surveillance programs, and computer-based clinical decision support systems that can be used for early detection of notifiable animal diseases. The development of DIVA-vaccines in the past 10 to 15 years has created, in principle, an excellent response instrument to counter intentional animal disease outbreaks. These developments have made our animal agriculture less vulnerable to agroterrorism. But we cannot relax; there are still many challenges, in particular with respect to integration of first line of defense, law enforcement, and early detection systems for animal diseases. © 2013, Mary Ann Liebert, Inc.

Nuotio L.,Finnish Food Safety Authority | Schneitz C.,Orion Corporation | Nilsson O.,National Veterinary Institute SVA
Poultry Science | Year: 2013

Extended-spectrum β-lactamases (ESBL) and class C serine β-lactamases (pAmpC) able to hydrolyze third-generation cephalosporins are a recognized threat to the efficacy of these drugs in treating serious infections. Broiler chicks are a known source of Escherichia coli harboring genes for these enzymes. Competitive exclusion (CE) has been used for decades in Finland to prevent the colonization of broiler ceca by Salmonella, but has not been widely used in Sweden. The markedly different prevalences of ESBL- or pAmpC-producing E. coli at slaughter in broilers produced in the 2 countries suggest a potential role for CE. The present study was undertaken to determine the efficacy of a commercial CE product in reducing the colonization of broiler ceca by ESBL- or pAmpC-producing E. coli. The challenge organisms were isolated from healthy broilers in Sweden. Each E. coli strain (1 ESBL and 2 pAmpC types) was subjected to 4 replicate trials. In each trial, a group of 20 newly hatched Ross breed chicks were treated by gavage with the CE product, whereas another group of 20 was left untreated. The next day, all 40 chicks were inoculated by gavage with the E. coli strain. The chicks were reared in cardboard boxes and received feed and water ad libitum. After a week the chicks were asphyxiated with CO2, and their ceca removed and examined for the presence of the E. coli strains. The median and quartiles of the challenge E. coli estimates in the groups were determined, and the treated and control groups were compared with the Wilcoxon 2-sample test. In each trial, a substantial and statistically significant or highly significant reduction was observed in the colonization of the ceca of CE- treated chicks by E. coli strains, compared with that of untreated control. Referring to an arbitrary criterion for high shedders presented in the literature, it was concluded that at least for the ESBL E. coli, the results were also of epidemiological relevance. © 2013 Poultry Science Association Inc.

Skarin H.,National Veterinary Institute SVA | Skarin H.,Swedish University of Agricultural Sciences | Segerman B.,National Veterinary Institute SVA
PLoS ONE | Year: 2014

Clostridium botulinum (group III), Clostridium novyi and Clostridium haemolyticum are well-known pathogens causing animal botulism, gas gangrene/black disease, and bacillary hemoglobinuria, respectively. A close genetic relationship exists between the species, which has resulted in the collective term C. novyi sensu lato. The pathogenic traits in these species, e.g., the botulinum neurotoxin and the novyi alpha toxin, are mainly linked to a large plasmidome consisting of plasmids and circular prophages. The plasmidome of C. novyi sensu lato has so far been poorly characterized. In this study we explored the genomic relationship of a wide range of strains of C. novyi sensu lato with a special focus on the dynamics of the plasmidome. Twenty-four genomes were sequenced from strains selected to represent as much as possible the genetic diversity in C. novyi sensu lato. Sixty-one plasmids were identified in these genomes and 28 of them were completed. The genomic comparisons revealed four separate lineages, which did not strictly correlate with the species designations. The plasmids were categorized into 13 different plasmid groups on the basis of their similarity and conservation of plasmid replication or partitioning genes. The plasmid groups, lineages and species were to a large extent entwined because plasmids and toxin genes had moved across the lineage boundaries. This dynamic process appears to be primarily driven by phages. We here present a comprehensive characterization of the complex species group C. novyi sensu lato, explaining the intermixed genetic properties. This study also provides examples how the reorganization of the botulinum toxin and the novyi alpha toxin genes within the plasmidome has affected the pathogenesis of the strains. © 2014 Skarin, Segerman.

Agren J.,National Veterinary Institute SVA | Agren J.,Swedish University of Agricultural Sciences | Sundstrom A.,National Veterinary Institute SVA | Hafstrom T.,National Veterinary Institute SVA | Segerman B.,National Veterinary Institute SVA
PLoS ONE | Year: 2012

The rapid development of Next Generation Sequencing technologies leads to the accumulation of huge amounts of sequencing data. The scientific community faces an enormous challenge in how to deal with this explosion. Here we present a software tool, 'Gegenees', that uses a fragmented alignment approach to facilitate the comparative analysis of hundreds of microbial genomes. The genomes are fragmented and compared, all against all, by a multithreaded BLAST control engine. Ready-made alignments can be complemented with new genomes without recalculating the existing data points. Gegenees gives a phylogenomic overview of the genomes and the alignment can then be mined for genomic regions with conservation patterns matching a defined target group and absent from a background group. The genomic regions are given biomarker scores forming a uniqueness signature that can be viewed and explored, graphically and in tabular form. A primer/probe alignment tool is also included for specificity verification of currently used or new primers. We exemplify the use of Gegenees on the Bacillus cereus group, on Foot and Mouth Disease Viruses, and on strains from the 2011 Escherichia coli O104:H4 outbreak. Gegenees contributes towards an increased capacity of fast and efficient data mining as more and more genomes become sequenced. © 2012 Ågren et al.

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