Oliver Bezuidt

Mainstreams of horizontal gene exchange in enterobacteria : consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011

Background Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods. Principal Findings The study revealed oscillations of gene exchange in enterobacteria, which originated from marine γ-Proteobacteria. These mobile genetic elements have become recombination hotspots and effective ‘vehicles’ ensuring a wide distribution of successful combinations of fitness and virulence genes among enterobacteria. Two remarkable peculiarities of the strain TY-2482 and its relatives were observed: i) retaining the genetic primitiveness by these strains as they somehow avoided the main fluxes of horizontal gene transfer which effectively penetrated other enetrobacteria; ii) acquisition of antibiotic resistance genes in a plasmid genomic island of β-Proteobacteria origin which ontologically is unrelated to the predominant genomic islands of enterobacteria. Conclusions Oscillations of horizontal gene exchange activity were reported which result from a counterbalance between the acquired resistance of bacteria towards existing mobile vectors and the generation of new vectors in the environmental microflora. We hypothesized that TY-2482 may originate from a genetically primitive lineage of E. coli that has evolved in confined geographical areas and brought by human migration or cattle trade onto an intersection of several independent streams of horizontal gene exchange. Development of a system for monitoring the new and most active gene exchange events was proposed.

Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB

BackgroundAdaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. In order to detect the impact of colonized habitats on P. aeruginosa microevolution we determined the genomic diversity between the highly virulent cystic fibrosis (CF) isolate CHA and two temporally and geographically unrelated clonal variants. The outcome was compared with the intraclonal genome diversity between three more closely related isolates of another clonal complex.ResultsThe three clone CHA isolates differed in their core genome in several dozen strain specific nucleotide exchanges and small deletions from each other. Loss of function mutations and non-conservative amino acid replacements affected several habitat- and lifestyle-associated traits, for example, the key regulator GacS of the switch between acute and chronic disease phenotypes was disrupted in strain CHA. Intraclonal genome diversity manifested in an individual composition of the respective accessory genome whereby the highest number of accessory DNA elements was observed for isolate PT22 from a polluted aquatic habitat. Little intraclonal diversity was observed between three spatiotemporally related outbreak isolates of clone TB. Although phenotypically different, only a few individual SNPs and deletions were detected in the clone TB isolates. Their accessory genome mainly differed in prophage-like DNA elements taken up by one of the strains.ConclusionsThe higher geographical and temporal distance of the clone CHA isolates was associated with an increased intraclonal genome diversity compared to the more closely related clone TB isolates derived from a common source demonstrating the impact of habitat adaptation on the microevolution of P. aeruginosa. However, even short-term habitat differentiation can cause major phenotypic diversification driven by single genomic variation events and uptake of phage DNA.

Distribution of horizontally transferred heavy metal resistance operons in recent outbreak bacteria

Mankind is confronted by the outbreaks of highly virulent and multi-drug resistant pathogens. The outbreak strains often belong to well-known diseases associated species such as Salmonella, Klebsiella and Mycobacterium, but even normally commensal and environmental microorganisms may suddenly acquire properties of virulent bacteria and cause nosocomial infections. The acquired virulence is often associated with lateral exchange of pathogenicity genomic islands containing drug and heavy metal resistance determinants. Metal ions are used by the immune system of macro-organisms against bactericidal agents. The ability to control heavy metal homeostasis is a factor that allows the survival of pathogenic microorganisms in macrophages. In this paper, we investigate the origin of heavy metal resistance operons in the recent outbreak strains and the possible routes which may lead to acquisitions of these genes by potentially new pathogens. We hypothesize that new outbreak microorganisms appear intermittently on an intersection of the non-specialized, genetically naïve strains of potential pathogens and virulence factor comprising vectors (plasmid and/or phages) newly generated in the environmental microflora. Global contamination of the environment and climate change may also have an effect toward the acceleration and appearance of new pathogens.

Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.

Abstract The Predicted Genomic Islands database (Pre_GI) is a comprehensive repository of prokaryotic genomic islands (islands, GIs) freely accessible at http://pregi.bi.up.ac.za/index.php . Pre_GI, Version 2015, catalogues 26 744 islands identified in 2407 bacterial/archaeal chromosomes and plasmids. It provides an easy-to-use interface which allows users the ability to query against the database with a variety of fields, parameters and associations. Pre_GI is constructed to be a web-resource for the analysis of ontological roads between islands and cartographic analysis of the global fluxes of mobile genetic elements through bacterial and archaeal taxonomic borders. Comparison of newly identified islands against Pre_GI presents an alternative avenue to identify their ontology, origin and relative time of acquisition. Pre_GI aims to aid research on horizontal transfer events and materials through providing data and tools for holistic investigation of migration of genes through ecological niches and taxonomic boundaries. Database URL: http://pregi.bi.up.ac.za/index.php , Version 2015

Draft Genome Sequence of Thermophilic Geobacillus sp. Strain Sah69, Isolated from Saharan Soil, Southeast Algeria

ABSTRACT Geobacillus spp. are potential sources of novel enzymes, such as those involved in the degradation of recalcitrant polymers. Here, we report a Geobacillus genome that may help reveal genomic differences between this strain and publicly available representatives of the same genus from diverse niches.

Whole genome sequence comparisons in taxonomoy

This chapter is devoted to the application of whole genome sequence comparisons in taxonomy. In principle there are three basic approaches: (1) genome indexes, increasingly used as an ‘in silico’ alternative to the experimental DNA–DNA hybridization (DDH); (2) gene content, its successful application depends on the number of genome sequences available for this analysis; and (3) multiple aligned (gene) sequence datasets. In this chapter, we have presented several methods that are practicable for the non-experienced scientist with a background in microbial taxonomy for estimating those genomic parameters. We are sure that further development in the field will facilitate use of genomics as an essential part of prokaryote taxonomy.

A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils

BackgroundSoil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity.MethodsWe used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs.ResultsIn total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and β-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r = − 0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events.ConclusionsARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments.

Optimization and Practical Use of Composition Based Approaches Towards Identification and Collection of Genomic Islands and Their Ontology in Prokaryotes

Abstract Motivation Horizontally transferred genomic islands (islands, GIs) have been referred to as important factors which contribute towards bacterial evolution in general and particularly towards the emergences of pathogens and outbreak instances. The development of tools for identification of such elements and retracing their distribution will help to understand how such cases arise. Sequence composition has been used to identify GIs, infer their phylogeny; and determine their relative time of insertion. Collection of metadata on known GIs will enhance insight into horizontal gene transfer ontology and flow. Results This paper introduces the merger of SeqWord Genomic Islands Sniffer (SWGIS), which utilizes composition based approaches for identification of GIs in bacterial genomic sequences, and the Predicted Genomic Islands (Pre_GI) database, which houses 26,744 islands found in 2,407 bacterial plasmids and chromosomes. SWGIS is a standalone program that detects GIs using a set of optimized parametric measures with estimates of acceptable false positive and false negative rates. Pre_GI is a novel repository that includes island ontology and flux. This study furthermore illustrates the need for parametric optimization towards the prediction of GIs to minimize false negative and false positive predictions. In addition Pre_GI emphasizes the practicality of the compounded knowledge that the database affords in detection and visualization of ontological links between GIs. Availability SWGIS is freely available on the web at http://www.bi.up.ac.za/SeqWord/sniffer/index.html , and Pre_GI is freely accessible at http://pregi.bi.up.ac.za/index.php.

Linguistic Approaches for Annotation, Visualization and Comparison of Prokaryotic Genomes and Environmental Sequences

Sequencing of bacterial genomes has become a common technique of the present day microbiology. Thereafter, data mining in complete genome sequence is an essential step to uncover the uniqueness and evolutionary success of microorganisms. Oligonucleotide usage (OU or k-mer) statistics provides invaluable tools to get insight into genome organization and functionality. The study of genome OU signatures has a long history dating back to early publications by Karlin et al. 1995, 1997, 1998, who focused mainly on dinucleotide compositional biases and their evolutionary implications. Statistical approaches of OU comparison were further advanced by Deschavanne et al., 1999, who applied chaos game algorithms; and by Pride et al., 2003, who extended the analysis to tetranucleotides using Markov Chain Model simulations. Later, a number of practical tools for phylogenetic comparison of bacterial genomes (Coenye & Vandamme, 2004; van Passel et al., 2006); identification of horizontally transferred genomic islands (Mrazek & Karlin, 1999; Pried & Blaser, 2002; Nakamura et al., 2004; Azad & Lawrence, 2005; Dufraign et al., 2005; Becq et al., 2007) and assignment of unknown genomic sequences (Abe et al., 2003; Teeling et al., 2004) based on OU statistics became publicly available. These approaches exploited the notion that genomic OU composition was less variable within genomes rather than between them, regardless of which genomic regions had been taken into consideration (Jernigan & Baran, 2002). A general belief was that if a significant compositional difference was discovered in genomic fragments relative to the core genome, these loci most likely can be assigned to horizontally transferred genetic elements (transposons, prophages or integrated plasmids). This approach was criticized by several researchers (Koski et al., 2001; Wang 2001), who pointed out that codon bias and base composition are poor indicators of horizontal gene transfer. Therefore, there is a need for more informative parameters which also take into account higher order DNA variation. An overview of the current OU statistical methods based on di-, tetraand hexanucleotides has been published recently (Bohlin et al., 2008). The conclusion of the review was that all methods were context dependent and, though being efficient and powerful, none of them were superior in all applications. Thus, the major

Long Non-coding RNAs in the Human Genome Acquired by Horizontal Gene Transfer

Results: Predicted genomic islands were enriched with long non-coding RNAs and also contributed to the acquisition and modification of proteins associated with the immune system and gonad development, albeit to a lesser extent. The estimated rate of acquisition of these genomic islands in vertebrate genomes was non-linear with regards to species divergence times with an acceleration at the time of vertebrate land invasion and during the transition of prosimians to monkeys soon after the Cretaceous-Paleogene extinction.