Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

Abstract

No single genealogical reconstruction or typing method currently encompasses all levels of bacterial diversity, from domain to strain. We propose ribosomal multilocus sequence typing (rMLST), an approach which indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes), as a means of integrating microbial genealogy and typing. As with multilocus sequence typing (MLST), rMLST employs curated reference sequences to identify gene variants efficiently and rapidly. The rps loci are ideal targets for a universal characterization scheme as they are: (i) present in all bacteria; (ii) distributed around the chromosome; and (iii) encode proteins which are under stabilizing selection for functional conservation. Collectively, the rps loci exhibit variation that resolves bacteria into groups at all taxonomic and most typing levels, providing significantly more resolution than 16S small subunit rRNA gene phylogenies. A web-accessible expandable database, comprising whole-genome data from more than 1900 bacterial isolates, including 28 draft genomes assembled de novo from the European Bioinformatics Institute (EBI) sequence read archive, has been assembled. The rps gene variation catalogued in this database permits rapid and computationally non-intensive identification of the phylogenetic position of any bacterial sequence at the domain, phylum, class, order, family, genus, species and strain levels. The groupings generated with rMLST data are consistent with current nomenclature schemes and independent of the clustering algorithm used. This approach is applicable to the other domains of life, potentially providing a rational and universal approach to the classification of life that is based on one of its fundamental features, the translation mechanism.

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

“…Advances in genomic sequencing technologies and analyses now allow a much greater precision in the taxonomic placement of strains (Jolley et al 2012;Kim et al 2014;Klenk and Göker 2010). The increasing affordability of next-generation sequencing technologies is resulting in a vast increase in the number of sequenced bacterial genomes.…”

“…However, many of the individual peaks that form a MALDI-TOF mass spectrum correspond to ribosomal proteins (RPs), which are encoded by more than 50 genes scattered in mostly chromosomal loci. RPs are ubiquitous and among the most abundant cytosolic proteins, regardless of the cell life stage or growth conditions (Ishihama et al 2008), and have masses mostly within the 4 to 30 kDa range that is examined with MALDI-TOF MS. Ribosomal multilocus sequence typing (rMLST) has been shown to be consistent with current bacterial nomenclature schemes and to provide accurate phylogenies for diverse taxonomic groups (Jolley et al 2012;Maiden et al 2013;Yutin et al 2012). These characteristics make RPs reliable biomarkers in MALDI-TOF MS analyses to obtain species and subspecies identification of diverse bacteria including bifidobacteria (Sato et al 2011), lactobacilli Teramoto et al 2007a), rhodococci (Teramoto et al 2009), members of the Sphingomonadaceae , and strains of Staphylococcus aureus (Josten et al 2013) and Neisseria meningitidis (Suarez et al 2013).…”

MLST revisited: the gene-by-gene approach to bacterial genomics

“…Other subsets of loci might have particular applications, such as conventional seven-locus MLST. It has been found that a scheme based on the 53 ribosomal protein loci present in most bacteria -ribosomal MLST (rMLST) -is both highly flexible and informative 75 .…”

“…For the purposes of bacterial typing and taxonomy, the ribosomal protein subunit (rps) genes have the advantages of being universally present but differentially variable 76 ; indeed, although the variability of some rps genes has prevented their inclusion in sets of core genes 77 , this variation permits high levels of discrimination among closely related isolates 30,75 . The rps genes have the further advantage of being distributed across the genome, offering some stability in the face of horizontal genetic transfer.…”

Making the genomic leap in HCT: application of second-generation sequencing to clinical advances in hematopoietic cell transplantation

“…Sequences derived from clinical isolates can then be queried against this database for rapid strain-level identification. 50 Unlike RT-PCR or array platforms, SGS detects a wide range of pathogens in a single test, eliminating single pathogen tests. This method is particularly helpful for the early detection and typing of fungal infections, which remain a major cause of morbidity and mortality in immunocompromised HCT recipients.…”