The hydrological context determines the beta-diversity of aerobic anoxygenic phototrophic bacteria in European Arctic seas but does not favor endemism

International audienceDespite an increasing number of studies over the last 15 years, aerobic anoxygenic photoheterotrophic (AAP) bacteria remain a puzzling functional group in terms of physiology, metabolism, and ecology. To contribute to a better knowledge of their environmental distribution, the present study aims at analyzing their diversity and structure at the boundary between the Norwegian, Greenland, and Barents Seas. The polymorphism of a marker gene encoding a sub-unit of the photosynthetic apparatus (pufM gene) was analyzed and attempted to be related to environmental parameters. The Atlantic or Arctic origin of water masses had a strong impact on the AAP bacterial community structure whose populations mostly belonged to the Alpha- and Gammaproteobacteria. A majority (>60%) of pufM sequences were affiliated to the Gammaproteobacteria reasserting that this class often represents the major component of the AAP bacterial community in oceanic regions. Two alphaproteobacterial groups dominate locally suggesting that they can constitute key players in this marine system transiently. We found that temperature is a major determinant of alpha diversity of AAP bacteria in this marine biome with specific clades emerging locally according to the partitioning of water masses. Whereas we expected specific AAP bacterial populations in this peculiar and newly explored ecosystem, most pufM sequences were highly related to sequences retrieved elsewhere. This observation highlights that the studied area does not favor AAP bacteria endemism but also opens new questions about the truthfulness of biogeographical patterns and on the extent of AAP bacterial diversity

Campylobacter : biological diagnosis and monitoring of resistance to antibiotics in France

The incidence of Campylobacter intestinal infections is currently very high, and still probably underestimated due to the limited use of detection tests and to problems associated with conditions and cost of the bacteria’s culture. However, any medical laboratory is able to diagnose a Campylobacter infection, and the three most frequent species (C. jejuni, C. coli and C. fetus) can be identified using simple criteria. Some campylobacter strains have become resistant to families of antibiotics used to treat human infections. It is therefore important to develop new molecular tools to improve detection and characterize the mechanisms involved in antibiotic resistance. The introduction of molecular biology has helped these processes and provided solutions to identify rare species as well as emergent pathogenic species.L'incidence des infections intestinales par des bactéries du genre Campylobacter est actuellement très élevée, même si elle est probablement sous-estimée, en raison de leur recherche occasionnelle, des conditions de culture et du coût. Le diagnostic d'une infection par Campylobacter est, cependant, à la portée de tout laboratoire de biologie médicale et le diagnostic d'espèce peut reposer sur des critères d'identification simples afin d'identifier les trois espèces les plus fréquentes (C. jejuni, C. coli et C. fetus). Les bactéries du genre Campylobacter ont développé des résistances à diverses familles d'antibiotiques d'intérêt thérapeutique chez l'homme. Il est important de développer de nouveaux outils moléculaires pour mieux détecter et caractériser les mécanismes de résistance impliqués. L'introduction de la biologie moléculaire a permis d'apporter des éléments de réponses à ce problème mais également de proposer des solutions dans l'identification des espèces rares ou de pathogènes émergents

Editorial: The Role of Mobile Genetic Elements in Bacterial Evolution and Their Adaptability

info:eu-repo/semantics/publishedVersio

Comparison of methods for detection of plasmid-mediated and chromosomally encoded colistin resistance in Enterobacteriaceae

Objectives: Because of the emergence of plasmid-mediated (mcr-1 and mcr-2 genes) and chromosomally encoded colistin resistance, reliable methods for detecting colistin resistance/susceptibility in routine laboratories are required. We evaluated the respective performances of the BD Phoenix automated system, the newly developed Rapid Polymyxin NP test and the broth microdilution (BMD) reference method to detect colistin resistance in Enterobacteriaceae, and particularly those producing mcr-1 and mcr-2.Methods: Colistin susceptibility of 123 enterobacterial clinical isolates (40 colistin-susceptible and 83 colistin-resistant isolates) was tested with the BD Phoenix automated system, the Rapid Polymyxin NP test and the BMD method. Molecular mechanisms responsible for plasmid-mediated and chromosomally encoded colistin resistance mechanisms were investigated by PCR and sequencing.Results: Considering BMD as a reference method, the BD Phoenix system failed to detect ten colistin-resistant isolates (one Escherichia coli, one Klebsiella pneumoniae, seven Enterobacter species and one Salmonella enterica). The Rapid Polymyxin NP test failed to detect the same single E. coli isolate. Those two latter methods detected the 16 E. coli, K. pneumoniae and S. enterica isolates producing the plasmid-encoded mcr-1 and mcr-2.Conclusions: The BD Phoenix system and the Rapid Polymyxin NP test are reliable techniques for detecting plasmid-mediated mcr-1 and mcr-2-related colistin resistance. However, a high rate of false susceptibility was observed with the BD Phoenix system, indicating that susceptibility results obtained with that system should be confirmed by BMD method. By contrast, the Rapid Polymyxin NP test showed a good agreement with the BMD method, and results were obtained rapidly (within 2 hours). The BMD method should be performed if minimum inhibitory concentration values are neede

Screening of Prophage Sequences Among Helicobacter Pylori

Until recently, Helicobacter pylori was considered a bacterium without prophages. The presence of an incomplete prophage sequence in strain B38 and a complete prophage sequence in strain B45 showed otherwise. Using a PCR strategy, based on degenerated primers designed after aligning bacteriophage integrase genes from H. pylori strains B38 and B45, and H. acinonychis prophage II, we found that integrase sequence was present in 21.4% (73/341) of the H. pylori clinical strains tested. The phylogenetic analysis of the sequenced region revealed that strains cluster according to their geographic origin, but not to their pathology. We have applied the same methodology to additional 147 European strains and 77 African strains, determining the presence of integrase sequence in 25.2% (37/147) of the former and in 19.5% (15/77) of the latter. Currently, we have a total of 565 strains screened for the presence of integrase gene, with 125 positive for this sequence (22.1%). To understand if these integrase sequences belong to reminiscent or complete prophages we are also screening for the presence of other prophage coding sequences. Among integrase positive strains, we found 19.2% (5/26) positive strains for the primase sequence and 53.3% (8/15) for the presence of the end of the phage. Presently, we are running the sequencing of the PCR amplified products in order to conduct the phylogenetic analysis. The results reinforce the abundance of prophages sequences in H. pylori and suggest that the majority of them belong to reminiscent prophages integrated within the bacterium genome

Dormant phages of Helicobacter pylori reveal distinct populations in Europe

Prophages of Helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. However, their role in the diversity of H. pylori strains is unknown. We demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between European populations, and that H. pylori prophages and their host bacteria share a complex evolutionary history. By comparing the phylogenetic trees of two prophage genes (integrase and holin) and the multilocus sequence typing (MLST)-based data obtained for seven housekeeping genes, we observed that the majority of the strains belong to the same phylogeographic group in both trees. Furthermore, we found that the Bayesian analysis of the population structure of the prophage genes identified two H. pylori European populations, hpNEurope and hpSWEurope, while the MLST sequences identified one European population, hpEurope. The population structure analysis of H. pylori prophages was even more discriminative than the traditional MLST-based method for the European population. Prophages are new players to be considered not only to show the diversity of H. pylori strains but also to more sharply define human populations.University of Malaya-Ministry of Education (UM-MoE) High Impact Research (HIR) Grant UM.C/HIR/MOHE/13/5 (h-50001-00-A000033) and by the Fundação para a Ciência e a Tecnologia (FCT) project grant PTDC/EBB-EBI/119860/2010

Des plantes tropicales qui forment des mares : les broméliacées-citerne : un écosystème aquatique miniature capital pour la biodiversité

Les plantes qui présentent des structures anatomiques permettant de retenir de l'eau en permanence sont assez répandues en milieu tropical. Si beaucoup sont maintenant cultivées pour être vendues en jardineries, faisant le bonheur des amateurs, elles forment en milieu naturel des écosystèmes aquatiques encore très peu étudiés et renferment une biodiversité que l'on est loin d'avoir recensée. En Amérique centrale et du Sud, les broméliacées-citerne, qui représentent les plus nombreuses et les plus diversifiées de ces "plantes-mares", permettent à des organismes très variés d'accomplir leur cycle de vie

Bacteriophage and H. pylori: an underestimated phenomena

Sem resumo disponível.publishe

Genome-wide identification of host-segregating SNPs for source attribution of clinical Campylobacter coli isolates

International audienceCampylobacter is among the most common causes of gastroenteritis worldwide. Campylobacter jejuni and Campylobacter coli are the most common species causing human-disease. DNA-sequence-based methods for strain characterization have focussed largely on C. jejuni, responsible for 80-90% of infections, meaning that C. coli epidemiology has lagged behind. Here we have analyzed the genome of 450 C. coli isolates to determine genetic markers that can discriminate isolates sampled from 3 major reservoir hosts (chickens, cattle and pigs). These markers were then applied to identify the source of infection of 147 C. coli from French clinical cases. Using STRUCTURE software, 259 potential host-segregating markers were revealed by probabilistic characterization of SNP frequency variation in strain collections from three different hosts. These SNPs were found in 41 genes or intergenic regions, mostly coding for proteins involved in motility and membrane functions. Source attribution of clinical isolates based on the differential presence of these markers confirmed chicken as the most common source of C. coli infection in France.IMPORTANCE Genome-wide and source attribution studies based on Campylobacter species have shown their importance for the understanding of foodborne infections. Although the use of MLST based on 7 genes from C. jejuni is a powerful method to structure populations, when applied to C. coli results have not clearly demonstrated their robustness. Therefore, we aim here to provide more accurate data based on the identification of single-nucleotide polymorphisms. Results from this study reveal an important number of host-segregating SNPs, found in proteins implied in motility, membrane functions or DNA repair systems. These findings offer new interesting opportunities for further study on C. coli adaptation to its environment. Additionally, the results demonstrate that poultry is potentially the main reservoir of C. coli in France

Comparison of methods for detection of plasmid-mediated and chromosomally encoded colistin resistance in Enterobacteriaceae.

Because of the emergence of plasmid-mediated (mcr-1 and mcr-2 genes) and chromosomally encoded colistin resistance, reliable methods for detecting colistin resistance/susceptibility in routine laboratories are required. We evaluated the respective performances of the BD Phoenix automated system, the newly developed Rapid Polymyxin NP test and the broth microdilution (BMD) reference method to detect colistin resistance in Enterobacteriaceae, and particularly those producing mcr-1 and mcr-2. Colistin susceptibility of 123 enterobacterial clinical isolates (40 colistin-susceptible and 83 colistin-resistant isolates) was tested with the BD Phoenix automated system, the Rapid Polymyxin NP test and the BMD method. Molecular mechanisms responsible for plasmid-mediated and chromosomally encoded colistin resistance mechanisms were investigated by PCR and sequencing. Considering BMD as a reference method, the BD Phoenix system failed to detect ten colistin-resistant isolates (one Escherichia coli, one Klebsiella pneumoniae, seven Enterobacter species and one Salmonella enterica). The Rapid Polymyxin NP test failed to detect the same single E. coli isolate. Those two latter methods detected the 16 E. coli, K. pneumoniae and S. enterica isolates producing the plasmid-encoded mcr-1 and mcr-2. The BD Phoenix system and the Rapid Polymyxin NP test are reliable techniques for detecting plasmid-mediated mcr-1 and mcr-2-related colistin resistance. However, a high rate of false susceptibility was observed with the BD Phoenix system, indicating that susceptibility results obtained with that system should be confirmed by BMD method. By contrast, the Rapid Polymyxin NP test showed a good agreement with the BMD method, and results were obtained rapidly (within 2 hours). The BMD method should be performed if minimum inhibitory concentration values are needed