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A novel approach for the identification and phylogenetic delineation of human Mycoplasma species and strains using genomic segment sequence analysis

Roachford, Orville St.E., Nelson, Karen E., Mohapatra, Bidyut R.
Infection, genetics, and evolution 2019 v.68 pp. 68-76
Mycoplasma, cost effectiveness, genomics, humans, immune system, molecular systematics, monitoring, morbidity, mucosa, operon, pathogens, phylogeny, ribosomal RNA, sequence analysis
Human Mycoplasma are opportunistic, facultative pathogens that are site-specific in their colonization of mucosal surfaces. They are responsible for significant annual morbidity in humans by causing acute illnesses and chronic auto-inflammatory diseases via modulation of the host's immune system. Accurate and reliable identification of Mycoplasma species and their strains are thus of upmost importance. This study, analysed for the first time, the effectiveness of a short (50 kb) genome fragment (termed as R-segment), which includes the complete rRNA operon and the flanking region up to 50 kb, as a single phylogenetic marker for assessing the molecular taxonomy and determining the identity of human Mycoplasma species and their strains. The R-segments of human mycoplasmas were shown to have inherent genetic properties [average nucleotide identity (ANI), codon bias index (CBI), genome-to-genome distances (GGD) and % G + C] similar to their whole genome counterparts. Based on the results of our R segment analysis, a species of human Mycoplasma can simply be defined as a group of strains that share R-segments with ANIs ≥97%. Additionally, R-segments offered superiority to 16S rRNA gene sequences and multilocus sequences for the delineation of the human Mycoplasma species and their strains. The overall comparative genomic results suggest that R-segment analysis can be considered as a promising cost-effective tool for the epidemiological surveillance and differentiation of the closely related species and/or strains of human mycoplasmas.