Staphylococcus petrasii subsp. pragensis subsp. nov., occurring in human clinical material

Švec, Pavel; Bel, Annelies De; Sedláček, Ivo; Petřáš, Petr; Gelbíčová, Tereza; Černohlávková, Jitka; Mašlanˇová, Ivana; Cnockaert, Margo; Varbanovová, Ivana; Echahidi, Fedoua; Vandamme, Peter; ̊ček, Roman Pantu

doi:10.1099/ijs.0.000220

Cited by 17 publications

(9 citation statements)

References 19 publications

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“…The description is the same as for Staphylococcus petrasii subsp. pragensis [57]. The DNA G+C content (mol%) of the type strain genome is 33.1 %, its approximate genome size is 2.45 Mbp, its GenBank accession is GCA_004785665.1.…”

Section: Description Of Staphylococcus Pragensis Sp Novmentioning

confidence: 99%

Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae

Madhaiyan

Wirth

Saravanan

2020

International Journal of Systematic and Evolutionary Microbiology

223

133

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Phylogenetic analyses based on 16S rRNA gene sequences of members of the family Staphylococcaceae showed the presence of para- and polyphyletic genera. This finding prompted a thorough investigation into the taxonomy of the Staphylococcaceae family by analysing their core genome phylogeny complemented with genome-based indices such as digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity. The resulting data suggested the following proposals: Auricoccus indicus was reduced in taxonomic rank as a later heterotypic synonym of Abyssicoccus albus ; Staphylococcus petrasii subsp. jettensis as a later heterotypic synonym of Staphylococcus petrasii subsp. petrasii ; the unification of Staphylococcus aureus subsp. anaerobius and Staphylococcus aureus subsp. aureus as Staphylococcus aureus ; the unification of Staphylococcus carnosus subsp. utilis and Staphylococcus carnosus subsp. carnosus as Staphylococcus carnosus ; the unification of Staphylococcus saprophyticus subsp. bovis and Staphylococcus saprophyticus subsp. saprophyticus as Staphylococcus saprophyticus ; Staphylococcus succinis subsp. casei as the novel species Staphylococcus casei; Staphylococcus schleiferi subsp. coagulans as the novel species Staphylococcus coagulans; Staphylococcus petrasii subsp. croceilyticus as the novel species Staphylococcus croceilyticus; Staphylococcus petrasii subsp. pragensis as the novel species Staphylococcus pragensis; Staphylococcus cohnii subsp. urealyticus as the novel species Staphylococcus urealyticus; the reassignment of Staphylococcus sciuri , Staphylococcus fleurettii , Staphylococcus lentus , Staphylococcus stepanovicii and Staphylococcus vitulinus to the novel genus Mammaliicoccus with Mammaliicoccus sciuri as the type species; and the formal assignment of Nosocomiicoccus as a member of the family Staphylococcaceae .

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Section: Description Of Staphylococcus Pragensis Sp Novmentioning

confidence: 99%

Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae

Madhaiyan

Wirth

Saravanan

2020

International Journal of Systematic and Evolutionary Microbiology

223

133

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“…Subspecies jettensis was recovered from wounds and implicated in bacteremia, whereas subspecies pragensis is believed to have caused prostatitis (23)(24)(25). One new species of coagulase-positive Staphylococcus, Staphylococcus argenteus, was isolated from the blood of a person in Australia.…”

Section: Gram-positive Coccimentioning

confidence: 99%

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Munson

Carroll

2017

J Clin Microbiol

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Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology. Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.KEYWORDS anaerobes, bacteria, Gram-negative bacteria, Gram-positive bacteria, taxonomy H uman microbiome studies, particularly those involving genome sequencing, have resulted in a seeming explosion of novel bacterial taxonomy. While many of these organisms appear to play a commensal role in site-specific ecology, some of the organisms may be of clinical significance in various patient populations. Moreover, enhanced studies of known bacterial genomes in a variety of applications, including those of an epidemiologic nature, have given rise to revisions and amendments to accepted bacterial taxonomy. Summaries of microbial taxonomy updates, such as those introduced in this edition of the Journal of Clinical Microbiology, are essential to routine practice in the clinical microbiology laboratory.Since 2014, laboratories subscribing to the College of American Pathologists accreditation program have encountered checklist standard MIC.11375 in the context of biennial inspection exercises. The standard (1) requires laboratories to assimilate "taxonomic changes that potentially affect the choice of appropriate antimicrobials to report and/or the interpretative breakpoints to use." Cited as an example for the context of this standard is the Gram-negative bacillus with the former taxonomic designation Actinobacillus actinomycetemcomitans. The taxonomic revision in 1985 (2) resulting in organism classification within the genus Haemophilus subsequently enabled antimicrobial susceptibility testing of clinically significant isolates using standards outlined in Table 2E of CLSI supplement M100S (example provided in [3]). Haemophilus test medium, with a 16-to 18-hour incubation in 5% CO 2 enrichment, could be utilized for disk diffusion. Haemophilus test medium broth could also be inoculated for broth microdilution testing with 20-to 24-hour incubation in ambient air.Subsequent reclassification of this organism into the genus Aggregatibacter (4) has resulted in the transition of susceptibility testing guidelines to those specific to (former) HACEK group organisms (Aggregatibacter spp., Cardiobacterium spp., Eikenella corrodens, and Kingella spp.) in Table 9 of the CLSI guideline M45 (5).

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“…For each of the top 10 most influential genera ( Table 1 ), the OTU that had the highest abundance in each genus bin was searched with MegaBLAST ( Morgulis et al, 2008 ) for highly similar sequences within the 16S rRNA sequence database from NCBI. For each sequence searched by MegaBLAST, the most highly similar sequence with information on source was summarized: genera found more frequently in Golden were associated with soil, horse dung, airborne dust, hard water, and clinical isolates ( Busse, 2003 ; Gallego, 2006 ; Kampfer, 2006 ; Muurholm et al, 2007 ; Smet et al, 2014 ); genera common to Sunshine are reported in swimming pool water, clinical material, cultivated land, and may be spore forming ( An et al, 2007 ; Furuhata et al, 2013 ; Amend et al, 2015 ; Echahidi et al, 2015 ; Im et al, 2015 ). Though Adonis showed no significant difference between samples with different storm-origins via the weighted Unifrac distance, there are obvious taxonomic differences between storm trajectories ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA

Honeyman

Day

Spear

2018

PeerJ

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Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture-independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfall’s geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual aeolian snowfall deposits of up to ∼10 kg of bacterial/archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes, and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the “everything is everywhere” hypotheses of the microbial world and that atmospheric transport of microbiota is not only common, but is capable of disseminating vast amounts of microbiota of different physiologies and genetics that then affect ecosystems globally. Snowfall, we conclude, is a significant repository of microbiological material with strong implications for both ecosystem genetic flux and general bio-aerosol theory.

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Staphylococcus petrasii subsp. pragensis subsp. nov., occurring in human clinical material

Cited by 17 publications

References 19 publications

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA

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