Niches, Population Structure and Genome Reduction in Ochrobactrum intermedium: Clues to Technology-Driven Emergence of Pathogens

Abstract

Ochrobactrum intermedium is considered as an emerging human environmental opportunistic pathogen with mild virulence. The distribution of isolates and sequences described in literature and databases showed frequent association with human beings and polluted environments. As population structures are related to bacterial lifestyles, we investigated by multi-locus approach the genetic structure of a population of 65 isolates representative of the known natural distribution of O. intermedium. The population was further surveyed for genome dynamics using pulsed-field gel electrophoresis and genomics. The population displayed a clonal epidemic structure with events of recombination that occurred mainly in clonal complexes. Concerning biogeography, clones were shared by human and environments and were both cosmopolitan and local. The main cosmopolitan clone was genetically and genomically stable, and grouped isolates that all harbored an atypical insertion in the rrs. Ubiquitism and stability of this major clone suggested a clonal succes in a particular niche. Events of genomic reduction were detected in the population and the deleted genomic content was described for one isolate. O. intermedium displayed allopatric characters associated to a tendancy of genome reduction suggesting a specialization process. Considering its relatedness with Brucella, this specialization might be a commitment toward pathogenic life-style that could be driven by technological selective pressure related medical and industrial technologies.

Taxonomic Organization of the Family Brucellaceae Based on a Phylogenomic Approach

“…16S rRNA-based analyses usually branch O. oryzae with O. pseudintermedium and O. gallinifaecis, away from the anthropi/tritici clade, although recA analyses provided results in agreement with our phylogenomic analysis (Scholz et al, 2008a;Huber et al, 2009;Gazolla Volpiano et al, 2019;Krzyżanowska et al, 2019). Similarly, O. pecoris usually branches within or as a sister taxon of Ochrobactrum Clade 2 (see below) in 16S rRNA-based phylogenies, with sometimes a close connection to O. rhizospherae and O. pituitosum (Kämpfer et al, 2011(Kämpfer et al, , 2013Krzyżanowska et al, 2019), while the MLST phylogeny more accurately branched it with the other members of Ochrobactrum Clade 1 (Aujoulat et al, 2014). For O. haematophilum, no single-locus or even multi-locus analysis could have resolved its correct position with high support (Scholz et al, 2008a;Aujoulat et al, 2014;Gazolla Volpiano et al, 2019), suggesting that its deep branching at the root of Clade 1 precludes from retrieving enough phylogenetic signal when only few genes are used.…”

“…could be drawn because of the underlying lack of phylogenetic resolution. Limited multilocus sequence typing (MLST) or Internal Transcribed Spacer (ITS) region-based analyses were also performed but were hampered by a small set of genes, a small set of species, or poorly supported branching, and still resulted in conflicting results (Zurdo-Pineiro et al, 2007;Aujoulat et al, 2014;Burygin et al, 2019;Gazolla Volpiano et al, 2019;Krzyżanowska et al, 2019). More recently, whole genome phylogenetic studies started to emerge but generally focused on a limited number of isolates of few species and could not provide a comprehensive view of the phylogenetic relationships at the family level or even at the Ochrobactrum genus level (Gazolla Volpiano et al, 2019;Krzyżanowska et al, 2019).…”

Identification and analysis of 5‐enolpyruvylshikimate‐3‐phosphate synthase (EPSPS) gene from glyphosate‐resistant Ochrobactrum intermedium Sq20

“…The genus Ochrobactrum belongs to the family Brucellaceae and Ochrobactrum intermedium is deemed an emerging human environmental opportunistic pathogen with mild virulence . Ochrobactrum strains are studied as potential bioremediation agents and plant growth‐promoting rhizobacteria .…”

“…The genus Ochrobactrum belongs to the family Brucellaceae and Ochrobactrum intermedium is deemed an emerging human environmental opportunistic pathogen with mild virulence. 42 Ochrobactrum strains are studied as potential bioremediation agents and plant growth-promoting rhizobacteria. [43][44][45][46][47] They are involved in the degradation of organophosphorus pesticides such as parathion and methylparathion, 48 phenol, 49 dimethylformamide (DMF, toxic organic solvent), 50 petroleum waste 51 and chlorothalonil.…”

Ochromobactrum intermedium: an emerging opportunistic pathogen—case of recurrent bacteraemia associated with infective endocarditis in a haemodialysis patient

“…The most common species identified is Ochrobactrum anthropi [1], [2]. They are widely regarded as environmental pathogens with low virulence [3], [4].…”