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International audience; ABSTRACT Fosfomycin is a decades-old antibiotic, currently reused because of its activity against multidrug-resistant bacteria. Here, we used a combined in vitro/in silico approach to search for fosfomycin resistance determinants in 25 new bacterial species isolated from the human microbiota. Putative resistance genes were cloned into a susceptible Escherichia coli strain. MIC values increased from 1 μg/ml to 1,024 μg/ml. Here, we report a new family of potential chromosomal fosfomycin resistance genes, named fosM .

International audience; Background/objectives High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored. Methods/subjects We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by tax-onogenomics and their genome sequenced. Results Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut. Conclusions High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.

Rickettsiae are obligate intracellular bacteria that can cause mild to life-threatening diseases, including epidemic typhus, one of the oldest pernicious diseases of mankind. Clinical awareness of rickettsial diseases and molecular diagnosis have shown that rickettsioses should be viewed as new emerging and reemerging diseases. Rickettsia has been shown to be a large genus with a worldwide distribution, a very diverse host range, including hosts that have no relationship with vertebrate. Genomic studies have demonstrated genome reduction due to gene loss associated with increased pathogenicity and horizontal DNA acquisition according to a sympatric mode of evolution in hosts that contain several organisms. This article presents a review of genotyping techniques and examines the principle of genotype determination in terms of taxonomic strategies and detection methods. This article summarizes the epidemiological and pathological features of Rickettsia and discusses the genomic findings that help the understanding of the evolution of pathogenicity including the deleterious mutations of repair systems and the toxin-antitoxin systems.

Coxiella burnetii, the causative agent of Q fever, may cause culture-negative vascular graft infections that can be diagnosed by serology and molecular biology. We present a case of vascular graft infection detected by positron emission tomography (PET) scanner. The presence of C. burnetii was confirmed by high antibody titers and positive polymerase chain reaction specific for C. burnetii. This report emphasizes the relevance of the PET scanner in the diagnosis of infection when used in association with Q fever serology and molecular biology for the etiological identification of C. burnetii.

International audience; The history of infectious diseases raised the plague as one of the most devastating for human beings. Far too often considered an ancient disease, the frequent resurgence of the plague has led to consider it as a reemerging disease in Madagascar, Algeria, Libya, and Congo. The genetic factors associated with the pathogenicity of Yersinia pestis, the causative agent of the plague, involve the acquisition of the pPCP1 plasmid that promotes host invasion through the expression of the virulence factor Pla. The surveillance of plague foci after the 2003 outbreak in Algeria resulted in a positive detection of the specific pla gene of Y. pestis in rodents. However, the phenotypic characterization of the isolate identified a Citrobacter koseri. The comparative genomics of our sequenced C. koseri URMITE genome revealed a mosaic gene structure resulting from the lifestyle of our isolate and provided evidence for gene exchanges with different enteric bacteria. The most striking was the acquisition of a continuous 2 kb genomic fragment containing the virulence factor Pla of the Y. pestis pPCP1 plasmid; however, the subcutaneous injection of the CKU strain in mice did not produce any pathogenic effect. Our findings demonstrate that fast molecular detection of plague using solely the pla gene is unsuitable and should rather require Y. pestis gene marker combinations. We also suggest that the evolutionary force that might govern the expression of pathogenicity can occur through the acquisition of virulence genes but could also require the loss or the inactivation of resident genes such as antivirulence genes.

Lactobacillus mucosae strain Marseille, isolated from stool samples of a child suffering from a malnutrition disorder called Kwashiorkor, produces bacteriocin and seems to have specific carbohydrate and lipid metabolisms different from those of other Lactobacillus organisms. The draft genome sequence of this strain is presented here.

Antibiotics and probiotics are widely used as growth promoters in agriculture. Most antibiotics prescribed in clinical practice are natural products that originate from Streptomyces spp, which were first used as agricultural probiotics. Antibiotics and probiotics both modify the gut microbiota. The effect of a probiotic species on the digestive flora depends on the strain and is largely determined by bacteriocin production. In human beings, as in animals, specific probiotics are associated with weight gain or loss. Improved understanding of the ability of specific probiotics to harvest energy from the host diet might lead to development of new treatments for obesity and malnutrition. In this Review, we present the effects of probiotics and antibiotics on the gut microbiota of human beings and animals and discuss their potential therapeutic use as interventions for weight gain and loss in human beings.

In the pregenomic era, the acquisition of pathogenicity islands via horizontal transfer was proposed as a major mechanism in pathogen evolution. Much effort has been expended to look for the contiguous blocks of virulence genes that are present in pathogenic bacteria, but absent in closely related species that are nonpathogenic. However, some of these virulence factors were found in nonpathogenic bacteria. Moreover, and contrary to expectation, pathogenic bacteria were found to lack genes (antivirulence genes) that are characteristic of nonpathogenic bacteria. The availability of complete genome sequences has led to a new era of pathogen research. Comparisons of genomes have shown that the most pathogenic bacteria have reduced genomes, with less ribosomal RNA and unorganized operons; they lack transcriptional regulators but have more genes that encode protein toxins, toxin-antitoxin (TA) modules, and proteins for DNA replication and repair, when compared with less pathogenic close relatives. These findings questioned the paradigm of virulence by gene acquisition and put forward the notion of genomic repertoire of virulence.

Q fever is a worldwide zoonosis caused by Coxiella burnetii. The clinical manifestations of Q fever include endocarditis, pneumonitis and hepatitis. Disease awareness and evolving diagnostic tests have enabled the recognition of unusual manifestations of Q fever. We report a case of Q fever osteomyelitis. A 51-year-old patient was admitted to hospital because of fever, leg weakness, and asthenia. His past medical history included surgery and a bone graft for the treatment of a giant cell tumor on the distal part of the femur. Blood and bone biopsy cultures were negative. Bone histological examination was consistent with a sub-acute or chronic inflammatory reaction that involved foci of epithelioid and gigantocellular infiltrates and necrosis. Serology testing revealed high antibody titers to C. burnetii antigens (phase I: IgG 3200; IgA 200; phase II: IgG 6400; IgA 400), which is indicative of chronic Q fever. The specific Polymerase Chain Reaction (PCR) of the abscess sample from the femoral region was positive for C. burnetii. The patient was treated for chronic Q fever with doxycycline and hydroxychloroquine for 18 months and recovered gradually without recurrence of pain or functional impairment. Q fever osteomyelitis is a rare and most likely underestimated disease. Epithelioid and gigantocellular granulomatous osteomyelitis in the context of culture-negative bone specimens should raise suspicion of Q fever. Serological tests, specific PCR and cell culture can provide evidence of a C. burnetii infection. Although bone diffusion may be a concern, the currently recommended treatment for Q fever was effective in this case.

Background Rickettsia prowazekii is the etiological agent of epidemic typhus and is an obligate intracellular bacterium that grows as a parasite freely within the cytoplasm of a eukaryotic host cell. Previous studies have shown that rOmpA and rOmpB which belong to the family of rickettsial cell surface antigens are involved in vitro in the adhesion of Rickettsiae to epithelial cells. Recently, two putative rickettsial adhesins have been identified using high resolution 2D-PAGE coupled with mass spectrometry. In this study, we further characterize and describe the adhesin Adr2 from R. prowazekii . Methodology/Principal findings Using an overlay assay coupled with mass spectrometry two adhesins, Adr1 (RP827) and Adr2 (RP828), were identified from the R. prowazekii proteome Recombinant R. prowazekii Adr2 was expressed through fusion with Dsbc in Escherichia coli , purified and concentrated, thus allowing production of specific monoclonal antibodies, as confirmed by western blot assays. Finally, inhibition of rickettsiae-induced cytotoxicity with monoclonal anti-Adr2 antibody has showed a greatest impact on bacterial cell entry at 8 h post-infection (ca50%) and then decreased progressively to attempt 18% of inhibition at day 7. These, correlated to the inhibition of rickettsiae-induced cytotoxicity with monoclonal anti-rOmpB antibody. Thus, Adr2 is sufficient to mediate R. prowazekii entry into the cell at early stage of mammalian cell infection. Conclusions Our results suggest that R. prowazekii Adr2 could be the main actor promoting the entry of rickettsiae into the host cells. The present study opens the framework for future investigations for better understanding of the Adr2 -mediated mechanisms involved in adhesion/invasion or intracellular survival of R. prowazekii .

Rickettsiae are obligate intracellular bacteria associated with arthropods, often pathogenic for humans. The Rickettsia genus belongs to the Alphaproteobacteria; it was divided into three major subgroups, mainly on the basis of phenotypic and serological features: the typhus group (TG), made of Rickettsia prowazekii and R. typhi, the spotted fever group (SFG) including R. conorii, R. africae, R. massiliae, R. akari, R. felis and several other validated species, and a group of marginal and divergent species including R. bellii and R. canadensis. Rickettsia spp. express few remarkable phenotypic characteristics. Therefore, their precise identification and phylogenetic classification have mainly relied on the analysis of molecular sequences. Phylogenetic analysis based on 16S rDNA gene sequences has frequently been

Bartonella rattimassiliensis is a facultative intracellular bacterium isolated from the blood of Rattus norvegicus in Marseille. The present study reports the draft genome of B. rattimassiliensis strain 15908 (CIP 107705 T ).

Bartonella rattaustraliani is a facultative intracellular bacterium isolated from the blood of a Rattus sp. in Australia. The present study reports the draft genome of B. rattaustraliani strain AUST/NH4 (CSUR B609 T ).