Giant mimiviruses escape many canonical criteria of the virus definition.

BACKGROUND: The discovery of mimivirus in 2003 prompted the quest for other giant viruses of amoebae. Mimiviruses and their relatives were found to differ considerably from other viruses. Their study led to major advances in virology and evolutionary biology. AIMS: We summarized the widening gap between mimiviruses and other viruses. SOURCES: We collected data from articles retrieved from PubMed using as keywords 'giant virus', 'mimivirus' and 'virophage', as well as quoted references from these articles. CONTENT: Data accumulated during the last 15 years on mimiviruses and other giant viruses highlight that there is a quantum leap between these infectious agents, the complexity of which is similar to that of intracellular microorganisms, and classical viruses. Notably, in addition to their giant structures and genomes, giant viruses have abundant gene repertoires with genes unique in the virosphere, including a tremendous set of translation components. The viruses contain hundreds of proteins and many transcripts. They share a core of central and ancient proteins but their genome sequences display a substantial level of mosaicism. Finally, mimiviruses have a specific mobilome, including virophages that can integrate into their genomes, and against which they can defend themselves through integration of short fragments of the DNA of these invaders. IMPLICATIONS: Mimiviruses and subsequently discovered giant viruses have changed the virus paradigm and contradict many virus definition criteria delineated for classical viruses. The major cellular hallmark that is still lacking in giant viruses is the ribosome, including both ribosomal protein and RNA encoding genes, which makes them bona fide microbes without ribosomes.

Bartonella henselae is usually not viable in lymph nodes of patients with cat scratch disease.

Bartonella henselae, the agent of cat scratch disease (CSD), appears to be a common organism responsible for lymphadenitis in both adults and children. There is a very low isolation rate for B. henselae from lymph nodes of patients with CSD. Our objective was to evaluate B. henselae viability in a large series of lymph nodes from patients with CSD. From January to November 2016, we analyzed lymph node biopsy samples from patients diagnosed with CSD. We used reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect B. henselae RNA, as well as cultures, histological analyses, and fluorescence in situ hybridization (FISH). We tested 87 lymph nodes positive for B. henselae DNA but only 8 (9%) presented with B. henselae RNA. We did not find a significant difference for the pap threshold cycle (CT) values between RNA-positive and RNA-negative lymph nodes (p = 0.5). Cultures, histological analyses, and FISH were negative for all the tested samples. We provide evidence that B. henselae are not or are rarely viable in most cases in the lymph nodes of patients with CSD.

Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing.

Recent studies using 16S rRNA gene amplification followed by clonal Sanger sequencing in cystic fibrosis demonstrated that cultured microorganisms are only part of the infecting flora. The purpose of this paper was to compare pyrosequencing and clonal Sanger sequencing on sputum. The sputum of a patient with cystic fibrosis was analysed by culture, Sanger clone sequencing and pyrosequencing after 16S rRNA gene amplification. A total of 4,499 sequencing reads were obtained, which could be attributed to six consensus sequences, but the length of reads leads to fastidious data analysis. Compared to clonal Sanger sequencing and to cultivation results, pyrosequencing recovers greater species richness and gives a more reliable estimate of the relative abundance of bacterial species. The 16S pyrosequencing approach expands our knowledge of the microbial diversity of cystic fibrosis sputum. The current lack of phylogenetic resolution at the species level for the GS 20 sequencing reads will be overcome with the next generation of pyrosequencing apparatus.

Multispacer typing technique for sequence-based typing of Bartonella quintana.

Bartonella quintana is a worldwide fastidious bacterium of the Alphaproteobacteria responsible for bacillary angiomatosis, trench fever, chronic lymphadenopathy, and culture-negative endocarditis. The recent genome sequencing of a B. quintana isolate allowed us to propose a genome-wide sequence-based typing method. To ensure sequence discrimination based on highly polymorphic areas, we amplified and sequenced 34 spacers in a large collection of B. quintana isolates. Six of these exhibited polymorphisms and allowed the characterization of 4 genotypes. However, the strain variants suggested by the noncoding sequences did not correlate with the results of pulsed-field gel electrophoresis (PFGE), which suggested a higher degree of variability. Modification of the PFGE profile of one isolate after nine subcultures confirmed that rearrangement frequencies are high in this species, making PFGE unreliable for epidemiological purposes. The low extent of sequence heterogeneity in the species suggests a recent emergence of this bacterium as a human pathogen. Direct typing of natural samples allowed the identification of a fifth genotype in the DNA extracted from a human body louse collected in Burundi. We have named the typing technique herein described multispacer typing.

Bartonella quintana and Mycobacterium tuberculosis coinfection in an HIV-infected patient with lymphadenitis.

Cat scratch disease (CSD) is usually associated with Bartonella henselae infection in patients with a history of cat exposure, but Bartonella quintana may also be a cause of chronic lympadenopathy in patients with cat or flea contact. The lymph node histopathology of CSD and tuberculosis may be indistinguishable. We report herein the first description of lymph node coinfection with B. quintana and M. tuberculosis in a 32-year HIV-infected woman. Culture of lymph node biopsy material on Columbia agar with sheep blood and on human endothelial cells in shell vial allowed us to isolate not only B. quintana, but also M. tuberculosis hominis.

Vertebral infections caused by Haemophilus aphrophilus: case report and review.

OBJECTIVE: To review in detail clinical presentation, bacteriologic findings, associated conditions and treatment of Haemophilus aphrophilus vertebral osteomyelitis and to compare them to a case we report herein. METHODS: A Medline (National Library of Medicine) search of the literature was performed by using the key words H. aphrophilus, spondylodiscitis, discitis, and vertebral osteomyelitis. The references of the case reports were examined for additional cases, especially those cited in older articles that had not been entered onto the bibliographic database. RESULTS: A case report of spondylodiscitis due to H. aphrophilus in a 35-year-old patient with a history of dental abscess 7 months before admission is presented. The patient responded well to treatment with ceftriaxone and ciprofloxacin. To date, only 14 cases of H. aphrophilus vertebral osteomyelitis have been reported. They are usually reported in middle-aged patients, usually male. Most recent cases have been treated with fluoroquinolones. Duration of treatment usually ranges from 1 to 3 months. CONCLUSIONS: H. aphrophilus is an uncommon cause of vertebral osteomyelitis. Patients are regularly cured by antibiotic therapy, provided that a tissue biopsy is performed in order to isolate the causative bacterium.

Culture and immunological detection of Tropheryma whippelii from the duodenum of a patient with Whipple disease.

CONTEXT: Culture of Tropheryma whippelii has been established only once, in human fibroblast cell lines from a heart valve inoculum. Molecular-based diagnostic techniques, although highly sensitive, may be less specific. New diagnostic tools involving isolation of bacteria from contaminated intestinal biopsies and immunohistological detection need to be developed. OBJECTIVE: To describe a novel method for detection and culture of T whippelii strains. DESIGN, SETTING, AND SUBJECTS: Laboratory analysis of duodenal biopsy specimens from a patient with typical relapsing Whipple disease with intestinal involvement, performed Marseille, France, in March 2000. Biopsy specimens were decontaminated with antimicrobial agents and inoculated onto cell cultures. Mouse anti-T whippelii polyclonal antibodies were used to detect T whippelii in fixed specimens taken from the patient before and after relapse, compared with specimens from 10 controls. The genotype of the isolate was determined by amplification and sequencing of 2 DNA fragments (ITS and 23S rRNA). MAIN OUTCOME MEASURE: Isolation and genotyping of a new strain(s) of T whippelii from the case patient's biopsy specimens. RESULTS: A strain was grown from the case patient's intestinal specimen that has a genotype different from the first strain isolated. During 2 episodes of Whipple disease, T whippelii bacteria were detected by immunochemistry in the patient's duodenal biopsy specimens, but not in controls. CONCLUSIONS: A second strain of T whippelii has been isolated and a protocol for isolation from the intestine has been proven to be efficient. Immunodetection of T whippelii in intestinal biopsy specimens may provide a useful tool for the diagnosis and follow-up of patients with Whipple disease. Both techniques need further evaluation and confirmation.

Isolation of Legionella anisa using an amoebic coculture procedure.

Conventional diagnostic tests for legionellosis were negative for a 61-year-old immunocompromised man with pneumonia. However, coculture of a sputum sample with Acanthamoeba polyphaga amoebae led to the recovery of Legionella anisa. This procedure may be a sensitive and convenient diagnostic method, especially for non-Legionella pneumophila species infections that can be diagnosed only by culture.

Culture of Bartonella quintana and Bartonella henselae from human samples: a 5-year experience (1993 to 1998).

Bartonella quintana and Bartonella henselae are fastidious gram-negative bacteria responsible for bacillary angiomatosis, trench fever, cat scratch disease, and endocarditis. During a 5-year period, we received 2,043 samples for culture of Bartonella sp. We found Bartonella sp. to be the etiologic agent in 38 cases of endocarditis, 78 cases of cat scratch disease, 16 cases of bacteremia in homeless people, and 7 cases of bacillary angiomatosis. We correlated the results of positive cultures with the clinical form of the disease, type of sample, culture procedure, PCR-based genomic detection, and antibody determination. Seventy-two isolates of B. quintana and nine isolates of B. henselae from 43 patients were obtained. Sixty-three of the B. quintana isolates and two of the B. henselae isolates, obtained from patients with no prior antibiotic therapy, were stably subcultured. The sensitivity of culture was low when compared with that of PCR-based detection methods in valves of patients with endocarditis (44 and 81%, respectively), skin biopsy samples of patients with bacillary angiomatosis (43 and 100%, respectively), and lymph nodes of cat scratch disease (13 and 30%, respectively). Serological diagnosis was also more sensitive in cases of endocarditis (97%) and cat scratch disease (90%). Among endocarditis patients, the sensitivity of the shell vial culture assay was 28% when inoculated with blood samples and 44% when inoculated with valvular biopsy samples, and the sensitivity of both was significantly higher than that of culture on agar (5% for blood [P = 0.045] and 4% for valve biopsy samples [P < 0.0005]). The most efficient culture procedure was the subculture of blood culture broth into shell vials (sensitivity, 71%). For patients with endocarditis, previous antibiotic therapy significantly affected results of blood culture; no patient who had been administered antibiotics yielded a positive blood culture, whereas 80% of patients with no previous antibiotic therapy yielded positive blood cultures (P = 0.0006). Previous antibiotic therapy did not, however, prevent isolation of Bartonella sp. from cardiac valves but did prevent the establishment of strains, as none of the 15 isolates from treated patients could be successfully subcultured. For the diagnosis of B. quintana bacteremia in homeless people, the efficiency of systematic subculture of blood culture broth onto agar was higher than that of direct blood plating (respective sensitivities, 98 and 10% [P < 10(-7)]). Nevertheless, both procedures are complementary, since when used together their sensitivity reached 100%. All homeless people with positive blood cultures had negative serology. The isolation rate of B. henselae from PCR-positive lymph nodes, in patients with cat scratch disease, was significantly lower than that from valves of endocarditis patients and skin biopsy samples from bacillary angiomatosis patients (13 and 33%, respectively [P = 0.084]). In cases of bacillary angiomatosis for which an agent was identified to species level, the isolation rate of B. henselae was lower than the isolation rate of B. quintana (28 and 64%, respectively [P = 0.003]). If culture is to be considered an efficient tool for the diagnosis of several Bartonella-related diseases, methodologies need to be improved, notably for the recovery of B. henselae from lymph nodes of patients with cat scratch disease.

Isolation of Legionella pneumophila by centrifugation of shell vial cell cultures from multiple liver and lung abscesses.

A 7-year-old girl was admitted to the hospital with acute lymphoblastic leukemia and was treated with allogenic cord blood transplantation. At day 30 after graft, she developed a fever and multiple nodular lesions disseminated in the liver and lungs. All bacterial cultures attempted on liver and lung biopsy specimens and blood remained sterile on standard axenic media. However, inoculation of liver and lung biopsy specimens on eukaryotic cell monolayers by the centrifugation-shell vial technique (M. Marrero and D. Raoult, Am. J. Trop. Med. Hyg. 40:197-199, 1989) led to the recovery of a strain of Legionella pneumophila serogroup 1, identified by 16S rRNA gene amplification and sequencing and serotyping. Our findings demonstrate that the centrifugation-cell culture method, which has previously been useful for the isolation of other strictly or facultatively intracellular bacteria, can also serve as a method for the recovery of L. pneumophila from clinical material.

[Clinical pilot study on repeated use of heparin, vancomycin, colimycine locked flush solution for central intravenous implanted catheter in oncology]. / Etude clinique pilote de l'utilisation repétée dune solution héparine, vancomycine, colimycine en verrouillage systématique des chambres implantables avec cathéter centeral en cancérologie.

With an anti-infectious and an antithrombotic prophylaxis aims, a locked flush solution including heparin and vancomycin, was used systematically for implantable venous access system for each patient, from january to april 1995. Since the 6th of april 1995, in order to widen the antibiotic spectrum on Gram negative bacteriae, we added colimycin at the flush solution. In 1995, 342 hospitalised patients held this type of venous access and received chemotherapy and/or radiochemotherapy for cancer. Two thousand six hundred thirty three manipulations were done, 575 with the first flush solution, 2058 with the second. During the year, 15 implantable access system (4.4%) were considered as infected, only 3 (0.9%) were removed, in the first period. THe infectious rate seemed to be stable, but the bacterial assessment to be modified between the two periods. The Gram negative bacterial infections seemed to decrease with colimycin addition (33% versus 50%). These results must be confirmed by a long term and/or randomized study.

Serological cross-reactions between Bartonella quintana, Bartonella henselae, and Coxiella burnetii.

The clinical manifestations of Q fever and bartonelloses can be confused, especially in cases of infectious endocarditis. Differential diagnosis of the diseases is important because the treatments required for Q fever and bartonelloses are different. Laboratory confirmation of a suspected case of either Q fever or bartonelloses is most commonly made by antibody estimation with an indirect immunofluorescence assay. With an indirect immunofluorescence assay, 258 serum samples from patients with Q fever were tested against Bartonella henselae and Bartonella quintana antigens, and 77 serum samples from patients with infection by Bartonella sp. were tested against Coxiella burnetii antigen. Cross-reactivity was observed: more than 50% of the chronic Q fever patients tested had antibodies which reacted against B. henselae antigen to a significant level. This cross-reaction was confirmed by a cross-adsorption study and protein immunoblotting. However, because the levels of specific antibody titers in cases of Bartonella endocarditis are typically extremely high, low-level cross-reaction between C. burnetii antibodies and B. henselae antigen in cases of Q fever endocarditis should not lead to misdiagnosis, provided serology testing for both agents is performed.