Philippe Riegel

Bartonella tribocorum sp. nov. : a new Bartonella species isolated from the blood of wild rats

Two Bartonella strains from blood of two wild rats (Rattus norvegicus) living in a rural environment were isolated. These strains were distinct from all previously known Bartonella species based on phenotypic and genotypic characteristics. This new species is distinguished by its trypsin-like activity, the absence of the ability to hydrolyse proline and tributyrin, its 16S rRNA and citrate synthase gene sequences and by whole-DNA hybridization data. This new species, for which the name Bartonella tribocorum sp. nov. is proposed, seems to be genetically related to Bartonella elizabethae, an agent isolated in a case of human endocarditis. The type strain of Bartonella tribocorum sp. nov. is IBS 506T (CIP 105476T).

Phylogeny of the Genus Corynebacterium Deduced from Analyses of Small-Subunit Ribosomal DNA Sequences

We determined almost complete small-subunit ribosomal DNA sequences of 50 reference strains belonging to the genera Corynebacterium, Rhodococcus, and Gordona and compared these sequences with previously published sequences. Three phylogenetic methods (the neighbor-joining, maximum-likelihood, and maximum-parsimony methods), as well as a bootstrap analysis, were used to assess the robustness of each topology which we obtained. The results of comparative phylogenetic analyses confirmed that the genera Corynebacterium, Dietzia, Gordona, Mycobacterium, Nocardia, Tsukamurella, and Turicella form a monophyletic taxon within the phylum containing the high-G+C-content gram-positive bacteria. The genus Corynebacterium appeared to be a monophyletic unit whose members could be divided into four major clusters. The validity of the genus Turicella is doubtful since members of this genus clearly belong to the genus Corynebacterium. The variability of chemotaxonomic characteristics within the genus Corynebacterium suggests that small-subunit ribosomal DNA sequence analysis is probably the most straightforward method for confirming that a bacterium belongs to this genus.

Nocardia pseudobrasiliensis sp. nov., a New Species of Nocardia Which Groups Bacterial Strains Previously Identified as Nocardia brasiliensis and Associated with Invasive Diseases

We studied five strains of a new Nocardia taxon recently identified among Nocardia brasiliensis strains associated with invasive diseases (R. J. Wallace, Jr., B. A. Brown, Z. Blacklock, R. Ulrich, K. Jost, J. M. Brown, M. M. McNeil, G. Onyi, V. A. Steingrube, and J. Gibson, J. Clin. Microbiol. 33:1528-1533, 1995) to determine their taxonomic status. Several characteristics of these organisms, including the presence of chemotype IV cell walls, nocardomycolic acids, a predominant menaquinone similar to that of Nocardia asteroides ATCC 19247T (T = type strain), and G+C contents ranging from 67 to 68 mol%, are characteristics of the genus Nocardia. Phylogenies based on small-subunit ribosomal DNA sequences clearly confirmed that all five strains belong to the genus Nocardia and occur on a single branch that is clearly distinct from N. brasiliensis. This branch forms a clade with Nocardia vaccinii, Nocardia nova, Nocardia otitidiscaviarum, and Nocardia seriolae. The five new strains exhibited high levels of DNA relatedness with each other, as determined by DNA-DNA hybridization experiments (S1 nuclease procedure), but not with N. brasiliensis strains or with strains of the four phylogenetically related Nocardia species mentioned above. The five new strains differ from N. brasiliensis in the following characteristics: mycolic acid pattern, decomposition of adenine, nitrate reduction, and antimicrobial agent susceptibilities. Therefore, we propose that these strains belong to a new species, Nocardia pseudobrasiliensis. The type strain is strain ATCC 51512, which was isolated from a leg abscess on a patient suffering from ulcerative colitis.

Coagulase-positive Staphylococcus pseudintermedius from animals causing human endocarditis

We report a case of infection with coagulase-positive Staphylococcus pseudintermedius related to the implantation of a cardioverter-defribrillator device. This species is usually isolated from infected animals, and contact with a dog was the probable source of infection in this patient. This isolate produced a leukotoxin effective against human polymorphonuclear leukocytes.

Corynebacterium freneyi sp. nov., alpha-glucosidase-positive strains related to Corynebacterium xerosis.

Three coryneform strains from clinical specimens were studied. They belonged to the genus Corynebacterium, since they had type IV cell walls containing corynemycolic acids. They had phenotypic characteristics that included alpha-glucosidase, pyrazinamidase and alkaline phosphatase activities and fermentation of glucose, ribose, maltose and sucrose. These are the characteristics of Corynebacterium xerosis. Since this species is very rare in human pathology, the strains were studied in more detail by comparing the 16S-23S intergenic spacers, rDNA sequences and levels of DNA similarity of these three strains and those of the reference strains C. xerosis ATCC 373T and Corynebacterium amycolatum CIP 103452T. According to DNA-DNA hybridization data, the three novel strains are members of the same species (level of DNA similarity >72%). Phylogenetic analysis revealed that these strains are closely related to C. xerosis and C. amycolatum, but DNA-relatedness experiments showed clearly that they constitute a distinct new species, with levels of DNA relatedness of less than 23% to C. xerosis ATCC 373T and less than 5% to C. amycolatum CIP 103452T. Two other alpha-glucosidase-positive strains presenting the same biochemical characteristics were included in the study and proved to be C. amycolatum. This new species can be differentiated from C. xerosis and C. amycolatum strains by carbon source utilization, intergenic spacer region length profiles and some biochemical characteristics such as glucose fermentation at 42 degrees C and growth at 20 degrees C. The name Corynebacterium freneyi sp. nov. is proposed with the type strain ISPB 6695110T (= CIP 106767T = DSM 44506T).

Corynebacterium Species Isolated from Bone and Joint Infections Identified by 16S rRNA Gene Sequence Analysis

ABSTRACT By the use of 16S rRNA gene sequence analysis we identified 28 of 31 Corynebacterium spp. isolated from bone and joint infections, including species never before isolated in such infections. Phenotypic analysis led to the correct identification of 8 of 31. 16S rRNA gene sequence analysis appears to be a good technique for identification of clinical strains of Corynebacterium spp.

Incidence and Pathogenic Effect of Streptococcus pseudopneumoniae

ABSTRACT We evaluated the incidence of Streptococcus pseudopneumoniae in clinical isolates by phenotypic methods and DNA-DNA hybridization. The pathogenic role of this organism was investigated with the mouse peritonitis/sepsis model. Our results show a low incidence (1/120 pneumococcal isolates) and a potential pathogenic effect for S. pseudopneumoniae.

Corynebacterium confusum sp. nov., isolated from human clinical specimens.

Three strains of a previously unknown coryneform bacterium were isolated from two patients with foot infections and from a blood culture of a third patient. The three non-lipophilic strains exhibited very slow fermentative acid production from glucose but not from maltose or sucrose, nitrate reductase activity, no tyrosinase activity and the presence of small amounts of tuberculostearic acid as the most significant phenotypic features. Differentiation of these strains from all other presently defined coryneform bacteria was readily achieved. Chemotaxonomic investigations revealed that the three strains unambiguously belonged to the genus Corynebacterium. Comparative 16S rRNA gene sequence analysis demonstrated that the isolates were almost identical and represented a new subline within the genus Corynebacterium, for which the designation Corynebacterium confusum sp. nov. is proposed. The type strain of Corynebacterium confusum is CCUG 38267T.

Implementation of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry in Routine Clinical Laboratories Improves Identification of Coagulase-Negative Staphylococci and Reveals the Pathogenic Role of Staphylococcus lugdunensis

ABSTRACT The use of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for staphylococcal identification is now considered routine in laboratories compared with the conventional phenotypical methods previously used. We verified its microbiological relevance for identifying the main species of coagulase-negative staphylococci (CoNS) by randomly selecting 50 isolates. From 1 January 2007 to 31 August 2008, 12,479 staphylococci were isolated with phenotypic methods, of which 4,594 were identified as Staphylococcus aureus and 7,885 were coagulase negative staphylococci. Using MALDI-TOF MS from 1 January 2011 to 31 August 2012, 14,913 staphylococci were identified, with 5,066 as S. aureus and 9,847 as CoNS. MALDI-TOF MS allowed the identification of approximately 85% of the CoNS strains, whereas only 14% of the CoNS strains were identified to the species level with phenotypic methods because they were often considered contaminants. Furthermore, the use of MALDI-TOF MS revealed the occurrence of recently characterized Staphylococcus species, such as S. pettenkoferi, S. condimenti, and S. piscifermentans. Microbiological relevance analysis further revealed that some species displayed a high rate of microbiological significance, i.e., 40% of the S. lugdunensis strains included in the analysis were associated with infection risk. This retrospective microbiological study confirms the role of MALDI-TOF MS in clinical settings for the identification of staphylococci with clinical consequences. The species distribution reveals the occurrence of the recently identified species S. pettenkoferi and putative virulent species, including S. lugdunensis.

Corynebacterium durum sp. nov., from Human Clinical Specimens

A new Corynebacterium species, Corynebacterium durum, was isolated from respiratory tract specimens of five human patients. The strains of this species exhibited similar morphologic and biochemical features that differentiated them from all recognized species. Notably, all of these strains developed irregular and strongly adherent colonies under aerobic conditions and produced acid from mannitol and galactose. The cells are long pleomorphic rods with some filaments. This species has characteristics of the genus Corynebacterium, such as 55 mol% guanine plus cytosine in the DNA and the presence of corynomycolic acids, meso-diaminopimelic acid, arabinose, and galactose in the cell wall. These isolates formed a homogeneous group in which the DNA-DNA similarity values (as determined by an S1 nuclease procedure) compared with reference strain IBS G15036T (T = type strain) ranged from 71 to 100%. The analysis of the nearly complete 16S rRNA gene sequence of IBS G15036T indicated that this new species represents a distinct taxon within the genus Corynebacterium. This new species can be identified on the basis of its colony morphology, fermentation of sugars, and enzymatic activities. Strain IBS G15036 (= CCUG 37331) is the type strain of C. durum.