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

2016 ◽  
Vol 55 (1) ◽  
pp. 24-42 ◽  
Author(s):  
Erik Munson ◽  
Karen C. Carroll
Keyword(s):  
Susceptibility Testing ◽  
Novel Species ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Taxonomic Status ◽  
Emerging Pathogens ◽  
Taxonomic Changes ◽  
Clinically Significant ◽  
Organism Identification ◽  
Evolutionary Microbiology

ABSTRACTTechnological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by theInternational 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 theJournal of Clinical Microbiologyon 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.

scholarly journals Evaluating performance of metagenomic characterization algorithms using in silico datasets generated with FASTQSim

2016 ◽  
Author(s):  
Anna Shcherbina ◽  
Darrell O. Ricke ◽  
Nelson Chiu
Keyword(s):  
In Silico ◽  
Microbial Community Composition ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Decision Makers ◽  
Emerging Pathogens ◽  
Read Mapping ◽  
Algorithm Performance ◽  
True Source ◽  
Organism Identification

AbstractBackgroundIn silico bacterial, viral, and human truth datasets were generated to evaluate available metagenomics algorithms. Sequenced datasets include background organisms, creating ambiguity in the true source organism for each read. Bacterial and viral datasets were created with even and staggered coverage to evaluate organism identification, read mapping, and gene identification capabilities of available algorithms. These truth datasets are provided as a resource for the development and refinement of metagenomic algorithms. Algorithm performance on these truth datasets can inform decision makers on strengths and weaknesses of available algorithms and how the results may be best leveraged for bacterial and viral organism identification and characterization.Source organisms were selected to mirror communities described in the Human Microbiome Project as well as the emerging pathogens listed by the National Institute of Allergy and Infectious Diseases. The six in silico datasets were used to evaluate the performance of six leading metagenomics algorithms: MetaScope, Kraken, LMAT, MetaPhlAn, MetaCV, and MetaPhyler.ResultsAlgorithms were evaluated on runtime, true positive organisms identified to the genus and species levels, false positive organisms identified to genus and species level, read mapping, relative abundance estimation, and gene calling. No algorithm out performed the others in all categories, and the algorithm or algorithms of choice strongly depends on analysis goals. MetaPhlAn excels for bacteria and LMAT for viruses. The algorithms were ranked by overall performance using a normalized weighted sum of the above metrics, and MetaScope emerged as the overall winner, followed by Kraken and LMAT.ConclusionsSimulated FASTQ datasets with well-characterized truth data about microbial community composition reveal numerous insights about the relative strengths and weaknesses of the metagenomics algorithms evaluated. The simulated datasets are available to download from the Sequence Read Archive (SRP062063).

scholarly journals Taxonomy and nomenclature of bacteria with clinical and scientific importance: current concepts for pharmacists and pharmaceutical scientists

2020 ◽  
Vol 89 (4) ◽  
pp. 99-108 ◽  
Author(s):  
Márió Gajdács
Keyword(s):  
Clinical Care ◽  
Bacterial Species ◽  
Data Interpretation ◽  
Bacterial Taxonomy ◽  
Novel Taxa ◽  
Taxonomic Changes ◽  
Clinically Significant ◽  
Living Organisms ◽  
Biological Methods ◽  
Testing Standards

Taxonomy is the science of the classification of various living organisms consisting of three independent, but interrelated disciplines, namely classification, nomenclature and identification. With the advent of molecular biological methods and sequencing, a revolution is currently occurring with regards to the reporting of novel taxa and changes in the taxonomy of already described bacterial species. The applications of taxonomic changes can be broad ranging: they may impact the clinical care of patients, through variations in choosing the appropriate antimicrobial susceptibility testing standards or data interpretation, or even their clinical relevance and epidemiology. The aim of this paper was to aid healthcare professionals and pharmaceutical scientists to navigate through the ‘maze’ of bacterial taxonomy, and to aid in finding authentic information regarding the description of taxonomic changes and to present some examples of changes in bacterial taxonomy which have proven to be clinically significant.

Nocardiosis With Brain Abscess Due to an Unusual Species, Nocardia transvalensis

2003 ◽  
Vol 127 (2) ◽  
pp. 224-226 ◽  
Author(s):  
Rebecca F. Yorke ◽  
Emilie Rouah
Keyword(s):  
Early Identification ◽  
Antibiotic Susceptibility ◽  
Susceptibility Testing ◽  
Subsequent Development ◽  
Pulmonary Involvement ◽  
Antibiotic Susceptibility Testing ◽  
Nocardia Species ◽  
Pathologic Findings ◽  
Brain Abscesses ◽  
Clinically Significant

Abstract The identification of Nocardia transvalensis, an unusual and probably underrecognized cause of nocardial infection, is clinically significant because of this species' resistance to aminoglycosides, a standard antinocardial therapy. Diagnosis requires analytic methods available predominately in reference laboratories. We report a case of disseminated infection with N transvalensis with primary pulmonary involvement and subsequent development of brain abscesses, and review the literature to date. Familiarity with the epidemiology, pathologic findings, and clinical significance of this and other unusual Nocardia species may increase early identification and antibiotic susceptibility testing in cases of nocardial infection.

scholarly journals Five-Year Longitudinal Assessment (2008 to 2012) of E-101 Solution Activity against Clinical Target and Antimicrobial-Resistant Pathogens

2014 ◽  
Vol 58 (8) ◽  
pp. 4911-4914 ◽  
Author(s):  
Gerald A. Denys ◽  
Chris M. Pillar ◽  
Daniel F. Sahm ◽  
Peter O'Hanley ◽  
Jackson T. Stephens
Keyword(s):  
Broad Spectrum ◽  
Susceptibility Testing ◽  
Bacterial Species ◽  
Clinical Isolates ◽  
Longitudinal Assessment ◽  
Gram Negative ◽  
Spectrum Activity ◽  
Eskape Pathogens ◽  
Negative Target ◽  
Broad Spectrum Activity

ABSTRACTThis study summarizes the topical E-101 solution susceptibility testing results for 760 Gram-positive and Gram-negative target pathogens collected from 75 U.S. sites between 2008 and 2012 and 103 ESKAPE pathogens. E-101 solution maintained potent activity against all bacterial species studied for each year tested, with MICs ranging from <0.008 to 0.25 μg porcine myeloperoxidase (pMPO)/ml. These results confirm that E-101 solution retains its potent broad-spectrum activity against U.S. clinical isolates and organisms with challenging resistance phenotypes.

scholarly journals Notification of changes in taxonomic opinion previously published outside the IJSEM

2012 ◽  
Vol 62 (1) ◽  
pp. 7-7 ◽  
Keyword(s):  
Scientific Community ◽  
International Committee ◽  
Editorial Office ◽  
New Combinations ◽  
Original Publication ◽  
The Public ◽  
Taxonomic Changes ◽  
The Creation ◽  
Evolutionary Microbiology

The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429–1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor. It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the ‘correct names’ (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no ‘official character’, other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.

scholarly journals Catalog of Rose Gall, Herb Gall, and Inquiline Gall Wasps (Hymenoptera: Cynipidae) of the United States, Canada, and Mexico

2021 ◽  
Author(s):  
Louis Nastasi ◽  
Andrew Deans
Keyword(s):  
United States ◽  
Taxonomic Status ◽  
Original Description ◽  
The United States ◽  
Valid Species ◽  
Vernacular Names ◽  
The North ◽  
Gall Wasps ◽  
Taxonomic Changes ◽  
Gall Induction

Cynipidae (Hymenoptera: Cynipoidea) is a diverse group of wasps, many of which are capable of inducing plants to make novel structures, galls, that protect and nourish the wasps' larvae. Other cynipids, especially those species in Ceroptresini and Synergini, are understood to be usurpers of galls made by other cynipids. The North American cynipid fauna has not been fully cataloged since 1979, but there is renewed interest in revising the taxonomy and in doing research that sheds light on the mechanisms of gall induction, the evolution of this life history, and their ecological interactions more broadly. Significant taxonomic changes have impacted the group since 1979, thereby warranting a new catalog. The current state of knowledge of species classified in Aulacideini, Ceroptresini, Diastrophini, Diplolepidini, Phanacidini, and Synergini in the United States, Canada, and Mexico is summarized in catalog format. We report 323 names, including 170 valid species of rose gall wasps, herb gall wasps, and inquiline gall wasps, classified in 12 genera, from the United States, Canada, and Mexico. Current taxonomic status, distribution, host associations, and vernacular names are listed for each species. The catalog also includes the original description of galls for many species of gall-inducer, as well as atomized characterizations of different gall traits as key-value pairs. For most galling species without existing vernacular names, new vernacular names are proposed.

scholarly journals Stenotrophomonas Nematodicola Sp. Nov., a Novel Intestinal Lifespan-Prolonging Bacterium for Caenorhabditis Elegans That Assists in Host Resistance to Bacillus Nematocida Colonization

2021 ◽  
Author(s):  
Rui Han ◽  
Yu Wang ◽  
Yang Deng ◽  
Yuqin Zhang ◽  
Lin Zhang ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Host Resistance ◽  
Type Strain ◽  
Novel Species ◽  
Bacterial Species ◽  
Intestinal Bacteria ◽  
Phenotypic Characteristics ◽  
Natural Habitats ◽  
Metagenomic Sequence ◽  
C Elegans

Abstract The soil-dwelling opportunistic bacterium Bacillus nematocida B16 shows comparatively strong killing activities against a variety of pathogenic nematodes. A bacterial strain CPCC 101271T, isolated from intestines of C. elegans in natural habitats, was found not only to be probiotics for C. elegans but also assist in resisting pathogen B16 infection. The lifespan of Caenorhabditis elegans fed on strain CPCC 101271T was extended by approximately 40% compared with that of worms fed on Escherichia coli OP50. In addition, the colonization of C. elegans by the pathogenic bacterium B. nematocida B16 was inhibited when it was pre-fed with strain CPCC 101271T. Based on a polyphasic taxonomy study including genotypic, chemotaxonomic and phenotypic characteristics, we propose that strain CPCC 101271T represents a novel bacterial species with the name Stenotrophomonas nematodicola sp. nov. and CPCC 101271T as the type strain. Metagenomic sequence analysis of the intestinal microbiota of C. elegans fed with strain CPCC 101271T and then infected with B16 revealed that pre-feeding with CPCC 101271T improved the diversity of intestinal bacteria, while the community structure varied significantly together with the fluctuation of Stenotrophomonas spp. and Bacillus spp. abundance during competition between strain CPCC 101271T and B16. In conclusion, the nematode microbiota strain CPCC 101271T, a novel species of the genus Stenotrophomonas, assisted in its host resistance to the pathogen Bacillus nematocida colonization, so as to act as an intestinal life span-prolonging for C. elegans.

scholarly journals Peritonitis Associated with Vancomycin-ResistantLactobacillus rhamnosus in a Continuous Ambulatory Peritoneal Dialysis Patient: Organism Identification, Antibiotic Therapy, and Case Report

1998 ◽  
Vol 36 (6) ◽  
pp. 1781-1783 ◽  
Author(s):  
Günter Klein ◽  
Edith Zill ◽  
Ralf Schindler ◽  
Jacobus Louwers
Keyword(s):  
Peritoneal Dialysis ◽  
Continuous Ambulatory Peritoneal Dialysis ◽  
Dialysis Patient ◽  
Susceptibility Testing ◽  
Lactobacillus Rhamnosus ◽  
Peritoneal Dialysis Patient ◽  
Antibiotic Susceptibility Testing ◽  
Coagulase Negative Staphylococci ◽  
Pure Cultures ◽  
Organism Identification

A case of Lactobacillus rhamnosus-associated peritonitis in a patient undergoing continuous ambulatory peritoneal dialysis is reported. The patient was treated with vancomycin after isolation of glycopeptide-susceptible coagulase-negative staphylococci. After a skin rash developed, vancomycin was discontinued and replaced with teicoplanin. Seven weeks after the glycopeptide therapy was discontinued, a Lactobacillus strain was isolated in pure cultures. The isolate was identified first incorrectly as L. acidophilus but later correctly as L. rhamnosus. Antibiotic susceptibility testing showed that the isolate was resistant to glycopeptides but susceptible to several other antibiotics. The antibiotic treatment was then switched to imipenem and was successful.

scholarly journals Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan

2004 ◽  
Vol 54 (6) ◽  
pp. 1927-1931 ◽  
Author(s):  
Akiko Kageyama ◽  
Katsukiyo Yazawa ◽  
Akira Mukai ◽  
Mari Kinoshita ◽  
Nobukatsu Takata ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Morphological Criteria ◽  
Respective Type ◽  
Type Strains

Three actinomycete strains isolated from soils and one strain isolated from a patient with lung nocardiosis in 1999 and 2001 in Japan have been provisionally assigned to the genus Nocardia on the basis of morphological criteria. These isolates were further investigated to determine their specific taxonomic status. Detailed chemotaxonomic characterization and 16S rRNA gene sequence analysis of these isolates confirmed that they belong to the genus Nocardia. The 16S rRNA gene sequences of the four strains were most similar to that of Nocardia farcinica. However, the sequence similarity values between these four strains and N. farcinica were <98·9 %. These four strains were susceptible to 5-fluorouracil, and they have the ability to decompose urea, which is a very characteristic trait. Furthermore, DNA–DNA relatedness data revealed that IFM 10311T, IFM 10312 and IFM 10313 comprise a single novel species of Nocardia, that IFM 10084T represents another novel species of Nocardia and that these two novel species could be distinguished from N. farcinica. The names Nocardia shimofusensis sp. nov. and Nocardia higoensis sp. nov. are proposed, with IFM 10311T (=NBRC 100134T=JCM 12122T=DSM 44733T) and IFM 10084T (=NBRC 100133T=JCM 12121T=DSM 44732T) as the respective type strains.

scholarly journals Prospective Evaluation of Light Scatter Technology Paired with Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Rapid Diagnosis of Urinary Tract Infections

2017 ◽  
Vol 55 (6) ◽  
pp. 1802-1811 ◽  
Author(s):  
Sandra Montgomery ◽  
Kiana Roman ◽  
Lan Ngyuen ◽  
Ana Maria Cardenas ◽  
James Knox ◽  
...  
Keyword(s):  
Susceptibility Testing ◽  
Automated System ◽  
Light Scatter ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tract Infections ◽  
Organism Identification ◽  
Tof Ms

ABSTRACTUrinary tract infections are one of the most common reasons for health care visits. Diagnosis and optimal treatment often require a urine culture, which takes an average of 1.5 to 2 days from urine collection to results, delaying optimal therapy. Faster, but accurate, alternatives are needed. Light scatter technology has been proposed for several years as a rapid screening tool, whereby negative specimens are excluded from culture. A commercially available light scatter device, BacterioScan 216Dx (BacterioScan, Inc.), has recently been advertised for this application. Paired use of mass spectrometry (MS) for bacterial identification and automated-system-based susceptibility testing straight from the light scatter suspension might provide dramatic improvement in times to a result. The present study prospectively evaluated the BacterioScan device, with culture as the reference standard. Positive light scatter specimens were used for downstream rapid matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS organism identification and automated-system-based antimicrobial susceptibility testing. Prospective evaluation of 439 urine samples showed a sensitivity of 96.5%, a specificity of 71.4%, and positive and negative predictive values of 45.1% and 98.8%, respectively. MALDI-TOF MS analysis of the suspension after density-based selection yielded a sensitivity of 72.1% and a specificity of 96.9%. Antimicrobial susceptibility testing of the samples identified by MALDI-TOF MS produced an overall categorical agreement of 99.2%. Given the high sensitivity and negative predictive value of results obtained, BacterioScan 216Dx is a reasonable approach for urine screening and might produce negative results in as few as 3 h, with no downstream workup. Paired rapid identification and susceptibility testing might be useful when MALDI-TOF MS results in an organism identification, and it might decrease the time to a result by more than 24 h.

Sign in / Sign up

Export Citation Format

Share Document