Taxonomie des bactéries anaérobies : De la reclassification à la découverte de nouveaux pathogènes

A reliable and up to date taxonomy is essential to unambiguously identify and differentiate human pathogenic microorganisms. Numerous new bacterial taxa have been created over the last years, meanwhile already known species or genus were reclassified, particularly concerning anaerobic bacteria. To clarify the taxonomic position of specific anaerobic bacteria displaying unusual antibiotic resistance, a polyphasic taxonomic approach combining the analysis of phenotypic, genotypic and phylogenetic markers has been used. This approach has been first applied to bacteria displaying low level resistance to vancomycin and belonging to the Clostridiaceae family. It resulted in the description of a new species of Tissierella as well as a new genus, Flavonifractor sp., which arises from the combination of two pre-existing species. Applied in a second time in a study on metronidazole resistance in Pretovella spp., this approach led to the discovery of a new species, Prevotella nanceiensis, the resistance of which to metronidazole has been implicated in therapeutic failure. A new gene (niml) coding a nitroimidazole reductase that seems to be intrinsic to the species Prevotella baroniae has also been described. This study emphasizes the importance of a clear and reliable taxonomy in medical bacteriology as well as the benefit of a polyphasic approach in taxonomy.Une classification et une nomenclature fiables et actualisées sont indispensables pour identifier et différencier les microorganismes pathogènes chez l'homme. Ces dernières années ont vu la création de nombreux nouveaux taxons bactériens ainsi que la reclassification d'espèces ou de genres déjà connus, notamment au sein des bactéries anaérobies. Afin de clarifier la position taxonomique de certains groupes de bactéries anaérobies pour lesquelles des phénotypes de résistance aux antibiotiques inhabituels étaient observés, une approche taxonomique mixte et consensuelle associant l'analyse de marqueurs phénotypiques, génotypiques, génomiques et phylogénétiques a été utilisée. Dans un premier temps, cette approche a été appliquée à des bactéries présentant un bas niveau de résistance à la vancomycine et appartenant aux Clostridiaceae, famille en plein remaniement taxonomique. Les résultats obtenus ont abouti à la description d'une nouvelle espèce de Tissierella et d'un nouveau genre, Flavonifractor, qui résulte du regroupement de deux espèces préexistantes. Appliquée dans le cadre d'une étude sur la résistance au métronidazole chez Prevotella spp., cette approche a conduit, dans un deuxième temps, à la découverte d'une nouvelle espèce, Prevotella nanceiensis, dont la résistance au métronidazole a été impliquée dans un échec thérapeutique. Un nouveau gène (nimI) codant une nitroimidazole réductase et a priori intrinsèque à l'espèce Prevotella baroniae a également été décrit. Ce travail souligne l'importance d'une taxonomie claire et fiable en bactériologie médicale et l'intérêt d'une approche mixte et consensuelle en taxonomie bactérienne

Diversité génétique et résistance aux antifongiques de Candida albicans lors du suivi de patients VIH +

MONTPELLIER-BU Pharmacie (341722105) / SudocSudocFranceF

Place de la PCR-hybridation dans le diagnostic de deux bactéries multirésistantes : les ERG et les SARM LPV

NANCY1-Bib. numérique (543959902) / SudocSudocFranceF

Metronidazole resistance and nim genes in anaerobes: A review

International audienceAcquired resistance to metronidazole, a 5-nitroimidazole drug largely used worldwide in the empirical treatment of infections caused by anaerobes, is worrisome, especially since such resistance has been described in multidrug-resistant anaerobic bacteria. In anaerobes, acquired resistance to metronidazole may be due to a combination of various and complex mechanisms. Among them, nim genes, possibly located on mobile genetic elements, encode nitro-imidazole-reductases responsible for drug inactivation. Since the first description of Nim proteins about 25 years ago, more nim genes have been identified; currently 11 nim genes are known (nimA to nimK). Mostly reported in Bacteroides fragilis group isolates, nim genes are now described in a variety of anaerobic genera encompassing the 4 main groups of Gram-negative and Gram-positive bacilli and cocci, with variable expression ranging from phenotypically silent to low-level or high-level resistance to metronidazole. This review describes the trends of metronidazole resistance rates among anaerobes over the past 20 years and summarizes current knowledge on mechanisms involved in this resistance. It also provides an update on the phylogenetic and geographical distribution of nim genes, the mechanisms involved in their expression and regulation, and their role in metronidazole resistance

A sequence database analysis of 5-nitroimidazole reductase and related proteins to expand knowledge on enzymes responsible for metronidazole inactivation

International audiencenim genes are associated, in combination with other factors, with acquired resistance to metronidazole (MTZ) in anaerobes. These genes encode 5-nitroimidazole reductase enzymes (Nim proteins) that reduce MTZ into an inactive compound. Eleven variants (nimA to nimK) are currently described in anaerobes with either a chromosomal or a plasmidic location. Mostly found in members of the Bacteroides fragilis group, nim genes were demonstrated in anaerobic taxa outside the phylum Bacteroidetes. Nitroreductase enzymes, weakly related to those found in Bacteroidetes but associated with MTZ inactivation, were also characterized both in anaerobic and non-anaerobic taxa. Published data only poorly reflect the growing number of data from cultivation-independent studies and sequences deposited in databases. Considering this limitation, we performed herein an analysis of the sequence databases with the aim to increase the current knowledge on Nim protein distribution and diversity. The 250 sequences the most closely related to the 11 known Nim proteins were selected and analyzed for identity level and phylogenetic relationships with Nim A to K proteins. The analysis revealed a larger diversity of anaerobic species harboring known Nim proteins than that currently described in the literature. Putative new variants of known Nim proteins and novel Nim proteins were found. In addition, nitroreductase proteins and homologs related to the pyridoxamine 5'-phosphate oxidase family were found in highly diverse anaerobic and aerobic taxa of human but also animal and environmental origin. On the other hand, we found a very low number of sequences recovered from metagenomic studies. Considering the different databases currently available to identify antimicrobial resistance genes (ARG) among metagenomic sequences, we hypothesized that this may, at least in part, be related to the incompleteness of ARG databases because none of them includes the 11 described nim genes at the time of our study. Both the wide distribution of proteins with potential MTZ inactivation ability within the bacterial world and a wider diversity of Nim determinants than expected from published literature is underlined in this sequence database analysis

In Silico Study of Cell Surface Structures of Parabacteroides distasonis Involved in Its Maintenance within the Gut Microbiota

The health-promoting Parabacteroides distasonis, which is part of the core microbiome, has recently received a lot of attention, showing beneficial properties for its host and potential as a new biotherapeutic product. However, no study has yet investigated the cell surface molecules and structures of P. distasonis that allow its maintenance within the gut microbiota. Moreover, although P. distasonis is strongly recognized as an intestinal commensal species with benefits for its host, several works displayed controversial results, showing it as an opportunistic pathogen. In this study, we reported gene clusters potentially involved in the synthesis of capsule, fimbriae-like and pili-like cell surface structures in 26 P. distasonis genomes and applied the new RfbA-typing classification in order to better understand and characterize the beneficial/pathogenic behavior related to P. distasonis strains. Two different types of fimbriae, three different types of pilus and up to fourteen capsular polysaccharide loci were identified over the 26 genomes studied. Moreover, the addition of data to the rfbA-type classification modified the outcome by rearranging rfbA genes and adding a fifth group to the classification. In conclusion, the strain variability in terms of external proteinaceous structure could explain the inter-strain differences previously observed of P. distasonis adhesion capacities and its potential pathogenicity, but no specific structure related to P. distasonis beneficial or detrimental activity was identified

Algorithm for rational use of Film Array Pneumonia Panel in bacterial coinfections of critically ill ventilated COVID-19 patients

International audienc

Parabacteroides distasonis Properties Linked to the Selection of New Biotherapeutics

Dysbiotic microbiota is often associated with health issues including inflammatory bowel disease or ulcerative colitis. In order to counterbalance host disorder caused by an alteration in the gut composition, numerous studies have focused on identifying new biotherapeutic products (NBPs). Among the promising NBPs is Parabacteroides distasonis, a gut microbiota member part of the core microbiome that recently has received much attention due to the numerous beneficial properties it brings to its host. In this study, the properties linked to the selection of NBPs were screened in 14 unrelated P. distasonis strains, including resistance to gastric conditions, adherence (Caco-2 model), transepithelial resistance (Caco-2 model), and immunomodulation, on nontreated and LPS-stimulated cells (HT-29 and peripheral blood mononuclear cells (PBMCs)). This approach allowed for the identification of five strains that combined almost all the in vitro biotherapeutic properties tested. However, all the P. distasonis strains induced the overproduction of proinflammatory cytokines on PBMCs, which was counteracted by the overproduction of the anti-inflammatory cytokines. Among these five strains, two particularly retained our attention as a potential NBP, by showing strong health-promoting function, the lowest overproduction of proinflammatory cytokines on PBMCs, and no detrimental effect on the host

Abdominal Aortic Aneurysm Infected by Yersinia pseudotuberculosis

Infected aneurysms caused by Yersinia are very uncommon and are principally due to Yersinia enterocolitica. We describe the first case of an infected aneurysm caused by Yersinia pseudotuberculosis in an elderly patient with a history of atherosclerotic cardiovascular disease

Evaluation of the New Vitek 2 ANC Card for Identification of Medically Relevant Anaerobic Bacteria▿

Of 261 anaerobic clinical isolates tested with the new Vitek 2 ANC card, 257 (98.5%) were correctly identified at the genus level. Among the 251 strains for which identification at the species level is possible with regard to the ANC database, 217 (86.5%) were correctly identified at the species level. Two strains (0.8%) were not identified, and eight were misidentified (3.1%). Of the 21 strains (8.1%) with low-level discrimination results, 14 were correctly identified at the species level by using the recommended additional tests. This system is a satisfactory new automated tool for the rapid identification of most anaerobic bacteria isolated in clinical laboratories