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Clonal analysis of the microflora associated with endodontic infections revealed a wide diversity of oral species.

Propionibacterium acnes subsp. acnes subsp. nov. and Propionibacterium acnes subsp. elongatum subsp. nov. are described. These emanate from the three known phylotypes of P. acnes, designated types I, II and III. Electron microscopy confirmed the filamentous cell shape of type III, showing a striking difference from types I/II, which were short rods. Biochemical tests indicated that, in types I/II, either the pyruvate, l-pyrrolidonyl arylamidase or d-ribose 2 test was positive, whereas all of these were negative among type III strains. Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectra, which profile mainly their ribosomal proteins, were different between these two groups. Surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) spectra of all phylotypes revealed a specific protein biomarker that was overexpressed in type III strains compared with types I/II only when grown aerobically. Reference strains had high whole-genome similarity between types I (>91 %) and II (>75 %), but a considerably lower level of 72 % similarity with type III. recA and gyrB sequence dendrograms confirmed the distant relatedness of type III, indicating the presence of two distinct centres of variation within the species P. acnes. On the other hand, cellular fatty acid profiles and 16S rRNA gene sequence relatedness (>99.3 %) circumscribed the species. Thus, we propose two subspecies, Propionibacterium acnes subsp. acnes subsp. nov. for types I/II and Propionibacterium acnes subsp. elongatum subsp. nov. for type III. The type strain of Propionibacterium acnes subsp. acnes is NCTC 737T ( = ATCC 6919T = JCM 6425T = DSM 1897T = CCUG 1794T), while the type strain of Propionibacterium acnes subsp. elongatum is K124T ( = NCTC 13655T = JCM 18919T).

hThe genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica. The Gram-negative Yersinia is one of the most important and well-studied bacterial genera, consisting of three human pathogens. Y. pestis is the causative agent of bubonic and pneumonic plague and is a recently diverged clone of Yersinia pseudotuberculosis (1), which alongside Y. enterocolitica is a zoonotic gastrointestinal pathogen (2). The remaining species are not associated with human disease and are considered to be environmental organisms, with the exception of the common fish pathogen Y. ruckeri (2) and the insecticidal species Y. entomophaga. Of the human-pathogenic species, Y. enterocolitica is the most common etiological agent of human disease, and in Germany and Scandinavia, the numbers of cases of human intestinal yersiniosis caused by Y. enterocolitica rival those caused by Salmonella (3). Y. enterocolitica is in itself a very diverse species that is classically subdivided into nonpathogenic, low-pathogenic, and high-pathogenic biotypes based on virulence in a mouse infection model (4). Biotype 1A isolates are considered nonpathogenic, which is concordant with a lack of the major Y. enterocolitica virulence factors such as pYV, invasin, YadA, and Ail (5), although there are numerous reports of biotype 1A human carriage (6, 7). Biotype 1B isolates are high pathogenic, which is concordant with carriage of the high-pathogenicity island, but isolation from human disease cases is very rare with the exception of notable outbreaks such as the recent emergence in Poland (8). Biotype 2 to 4 isolates are low pathogenic and are globally the most common causes of human gastrointestinal yersiniosis (4). Biotype 5 isolates are also considered low pathogenic but have only been isolated from wild hare populations and are very rare in nature (5).From a clinical perspective, the isolation and subsequent identification of Yersinia and in particular Y. enterocoli...