Comparative genomic analysis of the emerging pathogen Streptococcus pseudopneumoniae: novel insights into virulence determinants and identification of a novel species-specific molecular marker

Abstract

31Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. 32 pneumoniae. While initially considered as a commensal species, it has been increasingly 33 associated with lower-respiratory tract infections and high prevalence of antimicrobial 34 resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing 35 methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). 36 Using phylogenetic and comparative genomic analyses of SMG genomes, we identified a new 37 molecular marker specific for S. pseudopneumoniae and absent from any other bacterial 38 genome sequenced to date. We found that a large number of known virulence and 39 colonization genes are present in the core S. pseudopneumoniae genome and we reveal the 40 impressive number of known and new surface-exposed proteins encoded by this species. 41 Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with 42 allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most 43 common resistances, were encoded by Tn916-like integrating conjugative elements and 44 Mega-2. Overall, we found a tight association of genotypic determinants of AMR as well as 45 phenotypic AMR with a specific lineage of S. pseudopneumoniae. Taken together, our results 46 sheds light on the distribution in S. pseudopneumoniae of genes known to be important during 47 invasive disease and colonization and provide insight into features that could contribute to 48 virulence, colonization and adaptation. 50Importance 51 S. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-52 respiratory tract infections and associated with chronic obstructive pulmonary disease 53 (COPD) and exacerbation of COPD. However, much remains unknown on its clinical 54 importance and epidemiology, mainly due to the lack of specific means to distinguish it from 55 S. pneumoniae. Here, we provide a new molecular marker entirely specific for S. 56 pseudopneumoniae. Furthermore, our research provides a deep analysis of the presence of 57 virulence and colonization genes, as well as AMR determinants in this species. Our results 58 provide crucial information and pave the way for further studies aiming at understanding the 59 pathogenesis and epidemiology of S. pseudopneumoniae. 61 62Streptococcus pseudopneumoniae is a close relative of the human pathogen 64 Streptococcus pneumoniae. It was first described in 2004 (1), and belongs to the mitis group 65 which includes 13 other species of which some are the most common colonizers of the oral 66 cavity, such as S. mitis, S. sanguinis, S. oralis and S. gordonii (2). An increasing number of 67 reports indicate that S. pseudopneumoniae is a potential pathogen, usually associated with 68 underlying conditions (3-5), and that it can be isolated from both invasive and non-invasive 69 sites (6-9). It has been shown to be virulent in a mouse peritonitis/sepsis model (10), and to be 70 the probable ca...