Atopobium
            deltae sp. nov., isolated from the blood of a patient with Fournier’s gangrene

Cools, Piet; Oyaert, Matthijs; Vaneechoutte, Mario; Laere, Emmanuel De; Vervaeke, Steven

doi:10.1099/ijs.0.065243-0

Cited by 21 publications

(13 citation statements)

References 21 publications

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“…Atopobium (Collins and Wallbanks, 1992 ; Cools et al, 2014 ), the type genus of Atopobiaceae (Gupta et al, 2013 ) appears to be paraphyletic in the phylogenomic tree (Figure 1 ) as Olsenella (Dewhirst et al, 2001 ; Kraatz et al, 2011 ) forms the sister group to A. parvulum and A. rimae with high support ; this relationship is also apparent in 16S rRNA gene phylogenies (Cools et al, 2014 ), in the latter case with insufficient resolution unless constrained (Supplementary File 2 ). The CCT shows a core Atopobium composed of A. minutum , the type species, A. deltae and A. fossor (the genome of A. deltae has yet to be sequenced); this clade was highly supported in the UCT.…”

Section: Resultsmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

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The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

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Section: Resultsmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

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“…For each strain, MALDI-TOF spectra were generated of eight spots of one μl-aliquots of cell extract as described previously [ 20 ]. Spectra were generated by the FlexAnalysis software (Bruker, Germany) and were exported as text files.…”

Section: Methodsmentioning

confidence: 99%

Epidemic Achromobacter xylosoxidans strain among Belgian cystic fibrosis patients and review of literature

Cools

Vranckx

et al. 2016

BMC Microbiol

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BackgroundAchromobacter xylosoxidans is increasingly being recognized as an emerging pathogen in cystic fibrosis. Recent severe infections with A. xylosoxidans in some of our cystic fibrosis (CF) patients led to a re-evaluation of the epidemiology of CF-associated A. xylosoxidans infections in two Belgian reference centres (Antwerp and Ghent). Several of these patients also stayed at the Rehabilitation Centre De Haan (RHC). In total, 59 A. xylosoxidans isolates from 31 patients (including 26 CF patients), collected between 2001 and 2014, were studied. We evaluated Matrix Assisted Laser Desorption Ionisation -Time of Flight mass spectrometry (MALDI-TOF) as an alternative for McRAPD typing.ResultsBoth typing approaches established the presence of a major cluster, comprising isolates, all from 21 CF patients, including from two patients sampled when staying at the RHC a decade ago. This major cluster was the same as the cluster established already a decade ago at the RHC. A minor cluster consisted of 13 isolates from miscellaneous origin. A further seven isolates, including one from a non-CF patient who had stayed recently at the RHC, were singletons.ConclusionsTyping results of both methods were similar, indicating transmission of a single clone of A. xylosoxidans among several CF patients from at least two reference centres. Isolates of the same clone were already observed at the RHC, a decade ago. It is difficult to establish to what extent the RHC is the source of transmission, because the epidemic strain was already present when the first epidemiological study in the RHC was carried out.This study also documents the applicability of MALDI-TOF for typing of strains within the species A. xylosoxidans and the need to use the dynamic cutoff algorithm of the BioNumerics® software for correct clustering of the fingerprints.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0736-1) contains supplementary material, which is available to authorized users.

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“…MALDI-TOF MS can identify these species, and the correct identification is important, as A. schaalii, the most common pathogen in the genus, is resistant to trimethoprim-sulfamethoxazole and ciprofloxacin, which are the agents commonly used for the treatment of urinary tract infections (42). Atopobium deltae, another novel Gram-positive anaerobe, was recovered from the blood of a patient with Fournier's gangrene (43). Most of the newly discovered Gram-negative anaerobes have not been clearly associated with clinical infections, except for the new genus and species Eisenbergiella tayi (44), which was associated with bacteremia in an elderly patient.…”

Section: Anaerobesmentioning

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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Atopobium deltae sp. nov., isolated from the blood of a patient with Fournier’s gangrene

Cited by 21 publications

References 21 publications

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Epidemic Achromobacter xylosoxidans strain among Belgian cystic fibrosis patients and review of literature

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

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