Integrative taxonomy and population genomics of Aeromonas media and related species. Integrative taxonomy of Aeromonas media group

The genus Aeromonas groups ubiquitous bacteria mainly found in aquatic habitats. Among the 30 species currently described in the genus, half were characterized since the latest edition of the Bergey’s Manual of Systematic Bacteriology in 2003. Moreover, taxonomy in the genus is subject to controversies leading to several reclassifications (e.g., Beaz-Hidalgo et al., 2013). Among required clarifications, one concerns the little-known Aeromonas media species. This species has been described in river freshwater (Allen et al., 1983) and was then found in sewage water, activated sludge, drinking water, animal and human (Figueira et al., 2011; Pablos et al., 2009; Picao et al., 2008; Roger et al., 2012a). Aeromonas media acts as an opportunistic emerging pathogen causing a wide spectrum of diseases in human and animals (Figueras and Beaz-Hidalgo, 2015; Beaz-Hidalgo et al., 2010). It causes skin ulcers in fish and diarrhea in human (Singh, 2000), but with lower prevalence than other clinically relevant Aeromonas species (Parker and Shaw, 2011; Figueras and Beaz-Hidalgo, 2015). However, prevalence of A. media may be underestimated in routine clinical diagnosis because its phenotype is very similar to that of A. caviae (Altwegg et al., 1990). Heterogeneity in A. media species was early recognized because it was split in two DNA-DNA hybridization groups (HG), HG5A and HG5B represented by strains Popoff 233 and 239 respectively. The type strain A. media CECT 4232T groups into HG5B whereas the reference strains for HG5A and HG5B, Popoff 239 (syn. A. caviae LMG 13459) and Popoff 233 (syn. A. caviae LMG 13464) (Popoff et al., 1981), have been proposed to be reclassified in A. media (Kuijper et al., 1989; Altwegg et al., 1990). These intra-species heterogeneity was confirmed by 16S rRNA gene, rpoB and gyrB sequencing that showed that A. media strains distributed into two subgroups corresponding to the HG subgroups (Küpfer et al., 2006). Considering phenotype, every HG5B strain but no HG5A strains utilize DL-lactate (Altwegg et al., 1990). Besides, the gyrB sequences of 2 strains very recently proposed as ‘A. rivipollensis’ sp. nov. (non-yet validated species; Marti and Balcázar, 2015) suggested that they belonged to HG5A. In addition, A. media displays distinctive features compared to other Aeromonas species: i) a genetic polymorphism showed by 7 gene-multilocus sequence analysis (MLSA) higher than that of other species within the genus (5.8% vs. a mean of 2.5% for other species) (Roger et al., 2012a), ii) a high heterogeneity in the tRNA genes intergenic spacers (Laganowska and Kaznowski, 2005), iii) one of the highest rate of intragenomic heterogeneity among rrn operons (Alperi et al., 2008; Roger et al., 2012b), and iv) a strikingly high diversity of rrn chromosomal distribution (Roger et al., 2012b). However, all above studies were not designed for assessing the heterogeneity in A. media and included a rather low number of A. media strains. This work aimed to perform an in-depth phenotypic, genetic and genomic characterization of a representative population of 40 strains from different habitats and geographical regions affiliated to A. media in order to reappraise their classification using an integrative taxonomical approach taking into consideration recombination events and lifestyles of these bacteria.