The Pathogenic Role of  Actinomyces  spp. and Related Organisms in Genitourinary Infections: Discoveries in the New, Modern Diagnostic Era

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Abstract

Actinomycosis is a chronic, suppurative, granulomatous infectious disease, caused by different species of Actinomyces bacteria. To date, 26 validly published Actinomyces species have been described as part of a normal human microbiota or from human clinical specimens. Due to the rapid spread of new, modern diagnostic procedures, 13 of 26 of these species have been described in this century and the Actinomycetaceae family has undergone several taxonomic revisions, including the introduction of many novel species termed Actinomyces-like organisms (ALOs). There is scarce data available on the role of these novel bacterial species in various infectious processes in human medicine. The aim of this review is to provide a comprehensive overview of Actinomyces and closely related organisms involved in human diseases—with a special focus on newly described species—in particular their role in genitourinary tract infections in females and males.

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BLAST-EXPLORER helps you building datasets for phylogenetic analysis

Alexis Dereeper, Stéphane Audic, Jean-Michel Claverie … (2010)

Background The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task. Results To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the Phylogeny.fr platform. Conclusions BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://www.phylogeny.fr

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Actinomycosis: etiology, clinical features, diagnosis, treatment, and management

Florent Valour, Agathe Sénéchal, Celine Dupieux … (2014)

Actinomycosis is a rare chronic disease caused by Actinomyces spp., anaerobic Gram-positive bacteria that normally colonize the human mouth and digestive and genital tracts. Physicians must be aware of typical clinical presentations (such as cervicofacial actinomycosis following dental focus of infection, pelvic actinomycosis in women with an intrauterine device, and pulmonary actinomycosis in smokers with poor dental hygiene), but also that actinomycosis may mimic the malignancy process in various anatomical sites. Bacterial cultures and pathology are the cornerstone of diagnosis, but particular conditions are required in order to get the correct diagnosis. Prolonged bacterial cultures in anaerobic conditions are necessary to identify the bacterium and typical microscopic findings include necrosis with yellowish sulfur granules and filamentous Gram-positive fungal-like pathogens. Patients with actinomycosis require prolonged (6- to 12-month) high doses (to facilitate the drug penetration in abscess and in infected tissues) of penicillin G or amoxicillin, but the duration of antimicrobial therapy could probably be shortened to 3 months in patients in whom optimal surgical resection of infected tissues has been performed. Preventive measures, such as reduction of alcohol abuse and improvement of dental hygiene, may limit occurrence of pulmonary, cervicofacial, and central nervous system actinomycosis. In women, intrauterine devices must be changed every 5 years in order to limit the occurrence of pelvic actinomycosis.

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Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Imen Nouioui, Lorena Carro, Marina García-López … (2018)

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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Journal

Journal ID (nlm-ta): Antibiotics (Basel)

Journal ID (iso-abbrev): Antibiotics (Basel)

Journal ID (publisher-id): antibiotics

Title: Antibiotics

Publisher: MDPI

ISSN (Electronic): 2079-6382

Publication date (Electronic): 17 August 2020

Publication date Collection: August 2020

Volume: 9

Issue: 8

Electronic Location Identifier: 524

Affiliations

[1 ]Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, 6720 Szeged, Hungary; gajdacs.mario@ 123456pharm.u-szeged.hu

[2 ]Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary

[3 ]Institute of Translational Medicine, Faculty of Medicine, University of Pécs, 7624 Pécs, Hungary

Author notes

[* ]Correspondence: zsoldiedit25@ 123456gmail.com or tidenabru@ 123456freemail.hu ; Tel.: +36-62-536-246

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Márió Gajdács https://orcid.org/0000-0003-1270-0365

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Publisher ID: antibiotics-09-00524

DOI: 10.3390/antibiotics9080524

PMC ID: 7459602

PubMed ID: 32824418

SO-VID: 9f7c6608-0421-48b3-b064-c1aed848f3aa

License:

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

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Date received : 20 June 2020

Date accepted : 15 August 2020

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BLAST-EXPLORER helps you building datasets for phylogenetic analysis

Actinomycosis: etiology, clinical features, diagnosis, treatment, and management

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

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