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The planarian species Schmidtea mediterranea is a flatworm living in freshwater that is used in the research laboratory as a model to study developmental and regeneration mechanisms, as well as antibacterial mechanisms. However, the cultivable microbial repertoire of the microbes comprising its microbiota remains unknown. Here, we characterized the bacterial constituents of a 10-year-old laboratory culture of planarian species S. mediterranea via culturomics analysis. We isolated 40 cultivable bacterial species, including 1 unidentifiable species. The predominant phylum is Proteobacteria, and the most common genus is Pseudomonas. We discovered that parts of the bacterial flora of the planarian S. mediterranea can be classified as fish pathogens and opportunistic human pathogens. [ABSTRACT FROM AUTHOR]

The planarian S. mediterranea is a platyhelminth with worldwide distribution that can regenerate any part of its body after amputation and has the capacity to eliminate a large spectrum of human bacterial pathogens. Surprisingly, the microbiota of S. mediterranea remains poorly investigated. Using the culturomics strategy to study the bacterial component of planarians, we isolated a new bacterial strain, Marseille-Q2390, which we characterized with the taxono-genomic approach that associates phenotypic assays and genome sequencing and analysis. Strain Marseille-Q2390 exhibited a 16S rRNA sequence similarity of 99.36% with Pedobacter kyungheensis strain THG-T17T, the closest phylogenetic neighbor. It is a white-pigmented, Gram-negative, and rod-shaped bacterium. It grows in aerobic conditions and belongs to the family Sphingobacteriaceae. The genome of strain Marseille-Q2390 is 5,919,359 bp-long, with a G + C content of 40.3%. By comparing its genome with other closely related strains, the highest Orthologous Average Nucleotide Identity (Ortho-ANI) and digital DNA-DNA hybridization (dDDH) values were 85.71% and 30.50%, respectively, which were found with Pedobacter soli strain 15-51T. We conclude that strain Marseille-Q2390T is sufficiently different from other nearby species to be classified within a new species for which we propose the name Pedobacter ghigonii sp. nov. [ABSTRACT FROM AUTHOR]

Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898T is catalase-positive and oxidase-negative. The major fatty acids detected are 12-methyl-tetradecanoic acid, 13-methyl-tetradecanoic acid, and hexadecanoic acid. Marseille-P9898T strain shared more than 98% sequence similarity with the Metabacillus niabensis strain 4T19T (98.99%), Metabacillus halosaccharovorans strain E33T (98.75%), Metabacillus malikii strain NCCP-662T (98.19%), and Metabacillus litoralis strain SW-211T (97.15%). Marseille-P9898 strain belongs to Metabacillus genus. Genomic analysis revealed the highest similarities with Ortho-ANI and dDDH, 85.76% with Metabacillus halosaccharovorans, and 34.20% with Bacillus acidicola, respectively. These results show that the Marseille-P9898T strain is a novel bacterial species from Metabacillus genus, for which we propose the name of Metabacillus schmidteae sp. nov. (Type strain Marseille-P9898T = CSUR P9898T = DSM 111480T). [ABSTRACT FROM AUTHOR]

Marseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T). [ABSTRACT FROM AUTHOR]

Pedobacter schmidteae sp. nov. strain EGT (Collection de Souches de l'Unité des Rickettsie CSUR P6417 = Colección Española de Cultivos Tipo CECT 9771) is a new Pedobacter species isolated from the planarian Schmidtea mediterranea. Schmidtea mediterranea are flatworms living in freshwater and exhibiting an unusual ability to regenerate amputated parts. To date, the gut microbiota of Schmidtea mediterranea remains poorly studied. Here, via the culturomics strategy that consists in using diversified culture conditions, we isolated a new bacterium, strain EG, that we characterized using the taxono-genomics approach that combines phenotypic assays and genome sequencing and analysis. Strain EG exhibits a 16S rRNA sequence similarity of 98.29% with Pedobacter nyackensis strain NWG-II14T, its closest neighbour with standing in nomenclature. It is an aerobic bacterium belonging to the family Sphingobacteriaceae. Colonies are small, round, smooth and transparent. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The genome sequence is 6,198,518 bp–long with a G + C content of 41.13%, and the Ortho-ANI and dDDH values when compared to P. nyackensis are 77.34% and 21.50%, respectively. Strain EGT exhibits unique characteristics that classify it as the type strain of new bacterial species for which we propose the name Pedobacter schmidteae sp. nov. [ABSTRACT FROM AUTHOR]

There is a discrepancy between antibiotic use in medicine and agriculture in the intertropical zone and frequency of antibiotic resistance in clinical bacteria in these countries. We provide evidence that glyphosate (a herbicide but also an antibiotic drug) could be a possible driver of antibiotic resistance in countries where this herbicide is widely used because of modification of the microbial environment. Emergence of resistance in bacteria and fungi is correlated with glyphosate use in the world over the last 40 years. [ABSTRACT FROM AUTHOR]

Highlights • No new class has been discovered since daptomycin in 1986. • The environmental resistome is ancient. • The majority of antibiotics come from soil-living organisms (bacteria and fungi). • Most antibiotics are non-ribosomally synthesised secondary metabolites. • The gut microbiota harbours thousands of biosynthetic gene clusters (BGCs). ABSTRACT Antimicrobial resistance is considered a major public-health issue. Policies recommended by the World Health Organization (WHO) include research on new antibiotics. No new class has been discovered since daptomycin and linezolid in the 1980s, and only optimisation or combination of already known compounds has been recently commercialised. Antibiotics are natural products of soil-living organisms. Actinobacteria and fungi are the source of approximately two-thirds of the antimicrobial agents currently used in human medicine; they were mainly discovered during the golden age of antibiotic discovery. This era declined after the 1970s owing to the difficulty of cultivating fastidious bacterial species under laboratory conditions. Various strategies, such as rational drug design, to date have not led to the discovery of new antimicrobial agents. However, new promising approaches, e.g. genome mining or CRISPR-Cas9, are now being developed. The recent rebirth of culture methods from complex samples has, as a matter of fact, permitted the discovery of teixobactin from a new species isolated from soil. Recently, many biosynthetic gene clusters were identified from human-associated microbiota, especially from the gut and oral cavity. For example, the antimicrobial lugdunin was recently discovered in the oral cavity. The repertoire of human gut microbiota has recently substantially increased, with the discovery of hundreds of new species. Exploration of the repertoire of prokaryotes associated with humans using genome mining or newer culture approaches could be promising strategies for discovering new classes of antibiotics. [ABSTRACT FROM AUTHOR]

Many obligate or facultative intracellular bacteria pose a critical problem in clinical microbiology diagnosis as a result of their fastidious growth or lack of growth in conventional culture media. Molecular diagnosis is based on the analysis and demonstration of nucleic acids (DNA and RNA). In the field of infectiology, it combines laboratory medicine with the technology of molecular genetics to identify infectious pathogens. Fluorescence in situ hybridization (FISH) is used for the detection and localization of nucleotide sequences in various samples while preserving cell integrity. For more than 30 years, FISH methods have in constant evolution with the development of rRNA-targeted probes and synthetic molecules, such as PNA, which have contributed to the development of this technique in various fields by research and diagnostic laboratories. We describe here a panel of infectious diseases due to intracellular bacteria for which FISH diagnosis has proven its effectiveness. FISH techniques were applied in cases of blood-culture-negative endocarditis, respiratory infections, gastrointestinal diseases, mycobacterial infections, highly pathogenic microorganisms and other fastidious bacteria such as spirochetes. FISH has been proven to be applicable to various samples and for diverse infectious diseases, it can be used as a complementary tool for the diagnosis of infectious diseases by intracellular and fastidious bacteria. [ABSTRACT FROM AUTHOR]

The determination of the trophic preferences of the Anopheles gambiae Giles (Diptera: Culicidae) is a decisive parameter for the monitoring and the prevention of malaria risk transmission. Currently, arthropod blood feeding sources are identified using immunological or molecular biology traditional techniques. Despite the effectiveness of these methods, they present several limitations, and notably, they are time-consuming and costly techniques. A recent study demonstrated that MALDI-TOF MS could be a useful tool for the identification of blood meal origins in freshly engorged mosquitoes. However, the limited number of blood vertebrate species tested to date, did not allow an assessment of the efficiency of MALDI-TOF MS in distinguishing blood MS spectra among close host species, such as humans versus primates. Therefore, in the present study, blood from ten distinct vertebrate host species, including four domestic species, four wild species, and two primates, was selected to control the reliability of MALDI-TOF MS based identification. Host blood species-specific MS profiles, up to 24 h post-feeding in engorged Anopheles abdomens, were confirmed. Blind tests underlined the high specificity of MS spectra for the recognition of each host species, preventing misidentification. Nevertheless, an accurate analysis of the results from MS spectra queried against the MS database revealed that the reliability of identification is directly linked to the comprehensiveness of the MS reference database. Finally, the rapidity, the low-cost reagents, the simplicity of data analysis, and the accuracy of the tool for blood origin determination, make this proteomic strategy a promising complementary method for the elucidation of host/vector interactions. [ABSTRACT FROM AUTHOR]

Abstract Rickettsia species are arthropod endosymbiotic α-proteobacteria that can infect mammalian hosts during their obligate intracellular lifecycle, and cause a range of mild to severe diseases in humans. Paradoxically, during their adaptation to a bottleneck lifestyle, rickettsial genomes have undergone an evolution marked by a progressive chromosomic and plasmidic degradation resulting in a genome reduction from 1.5 to 1.1 Mb, with a coding capacity of 69–84%. A striking finding of rickettsial genomics has been that the most virulent species had genomes that were drastically reduced and degraded when compared to closely related less virulent or nonpathogenic species. This paradoxical evolution, which is not unique to members of the genus Rickettsia but has been identified as a convergent evolution of several major human pathogenic bacteria, parallels a selected loss of genes associated with transcriptional regulators, but with a high preservation of toxin-antitoxin (TA) modules and recombination and DNA repair proteins. In addition, these bacteria have undergone a proliferation of genetic elements, notably short palindromic elements, whose role remains unknown. Recent proteomic and transcriptomics analyses have revealed a differential level or degradation of gene expression that may, at least partially, explain differences in virulence among Rickettsia species. However, future investigations are mandatory to provide novel insights into the mechanisms by which genomic reductive evolution contributes to an emergence of pathogenesis. [ABSTRACT FROM AUTHOR]

My opinion is that hydroxychloroquine has become the symbol of a struggle between practising physicians and methodologists [[1]], and the Western world against the rest of the world [[2]]. Indeed in this journal, as for hydroxychloroquine, it was reported that one meta-analysis demonstrates no effect of hydroxychloroquine on COVID-19 infection [[21]] and the other the opposite [[22]]. In conclusion, there are currently nearly 100 publications available in the literature evaluating, through randomized or observational studies, or big data analyses, the effect of hydroxychloroquine on patients generating opposite results. The effect of drugs, in most viral diseases (such as zoster, for example), is different: at the beginning, where antivirals are effective; at the time of the inflammatory reaction, where corticosteroid therapy is effective; and at the time of necrotic lesions, where no treatment is effective. [Extracted from the article]

Background/Purpose(s). We have extensively used HCQ at 200 mg three times a day (tid) to treat various infections such as Q fever and Whipple's disease. Serum levels of between 1 μg/ml and 2 μg/ml serum level are recommended to achieve the safety and efficacy of these treatments. Our aim in this paper is to describe our experience regarding the pharmacokinetics and toxicity of HCQ in another infection caused by SARS-CoV-2. Methods. As recommended, we performed electrocardiograms before administering HCQ off-label. The HCQ concentration in the serum was monitored to ensure the effectiveness and safety of the treatment. We retrospectively analysed HCQ serum concentrations measured over time and toxicity data in patients with COVID-19 who were treated with HCQ at the IHU Marseille Infection. We did not treat patients with HCQ contraindications with this medication. Results. We measured HCQ concentrations in 1310 serum samples from 989 patients with COVID-19. The mean ± SD HCQ concentration increased in patients' sera during treatment from day 1 (0.10 μg/ml ± 0.08) to day 11 (0.85 μg/ml ± 0.44), confirming that HCQ accumulates in the body during short-term therapy. However, the observed concentrations did not exceed the therapeutic range for other indications (0.80–1.20 μg/mL in Q fever patients treated for between 18 and 24 months). In patients treated with HCQ, major side effects included intestinal disorders (nausea, vomiting, and gastric pain) and QT prolongation. No conduction disorders (including torsades de pointes and ventricular arrhythmia), cardiomyopathy, retinopathy, or HCQ-related deaths were observed. Conclusions. In patients treated over a short time period with 200 mg tid of HCQ, therapeutic concentrations in serum were obtained in most patients without significant side effects or complications. Although patients must be carefully evaluated for HCQ contraindications, HCQ 200 mg tid for ten days can be considered an appropriate and safe dosage in patients with COVID-19. [ABSTRACT FROM AUTHOR]

Obesity represents a worldwide public health crisis. Trials suggested that intestinal microbiota may contribute to the development of obesity and highlighted the involvement of bacteria, including Lactobacillus spp., in changes to the host metabolism. Several experiments have shown significant effects of Lactobacillus probiotics on weight modification. Lactobacillus spp. are involved in the digestion of complex carbohydrates not digested by the host in the colon and also participate in the degradation of lipids and simple sugars in the duodenum and jejunum. Moreover, Lactobacillus species survive throughout the gastrointestinal tract, as they are able to survive in the presence of bile and low pH, and produce an antimicrobial agent, allowing them to reduce the number of bacteria in the gut. Hence, Lactobacillus spp. can have a significant impact on microbiota and, consequently, on weight change. Here, we review current studies of Lactobacillus spp. involved in weight change and discuss the different mechanisms of action by which Lactobacillus spp. acts on host digestion and appears to influence weight. [ABSTRACT FROM AUTHOR]

Aerosols from the products of abortions of infected animals with Coxiella burnetii were known to be the main source of infection in humans with this bacterium. However, little is known about the excretion of C. burnetii in the feces and urine of infected mice, or the dynamic of transmission between infected and healthy mice. To investigate whether C. burnetii can be excreted in the feces and urine of infected mice and whether transmission to uninfected cage mates occurs, male mice were inoculated with C. burnetii using a “whole body aerosol system” and feces and urine were collected different time points post-infection from these mice. One hour post exposure to aerosols, uninfected mice was placed with infected mice and the transmission was monitored using blood, and organs biopsies collected after sacrifice of contact mice different time points post-contact. Bacterial DNA was not detected in the feces and urine of infected mice at 3, 7, 14 and 28 days post-inoculation suggesting that C. burnetii was not excreted in the feces and urine and consequently they cannot be source of contamination. However, based on the positive PCR results for lungs, blood, spleen, tracheal lymph nodes and cervical lymph nodes, some of the contact animals were considered contaminated at 8 days post-contact. These results indicated that transmission of C. burnetii to contact animals occurs, and it is unlikely that feces and urine act as source of this transmission. Further experiments are needed to clarify the exact mode of contamination. [ABSTRACT FROM AUTHOR]

Putatively, stem–loop RNA hairpins explain networks of selfish elements and RNA world remnants. Their genomic density increases with intracellular lifestyle, especially when comparing giant viruses and their virophages. RNA protogenomes presumably templated for mRNAs and self-replicating stem–loops, ancestors of modern genes and parasitic sequences, including tRNAs and rRNAs. Primary and secondary structure analyses suggest common ancestry for t/rRNAs and parasitic RNAs, parsimoniously link diverse RNA metabolites (replication origins, tRNAs, ribozymes, riboswitches, miRNAs and rRNAs) to parasitic RNAs (ribosomal viroids, Rickettsia repeated palindromic elements (RPE), stem–loop hairpins in giant viruses, their virophages, and transposable retrovirus-derived elements). Results indicate ongoing genesis of small RNA metabolites, and common ancestry or similar genesis for rRNA and retroviral sequences. Assuming functional integration of modular duplicated RNA hairpins evolutionarily unifies diverse molecules, postulating stem–loop hairpin RNAs as origins of genetic innovation, ancestors of rRNAs, retro- and Mimivirus sequences, and cells. [ABSTRACT FROM AUTHOR]

Background: Klebsiella pneumoniae is a Gram-negative bacterial species well known for its capacity to cause infections in humans, and to carry and spread a wide variety of resistance genes including extended-spectrum beta-lactamase genes, carbapenem resistance genes, and colistin resistance genes. Recently, our real-time laboratory-based surveillance system MARSS (the Marseille Antibiotic Resistance Surveillance System) allowed us to observe a intringing dramatic decrease in the beta-lactam resistance level of the K. pneumoniae strains routinely isolated from patients hospitalized in our settings since 2013. Here we study the evolution of the prevalence of K. pneumoniae infections in Marseille university hospitals, France, from January 2012 to July 2015, and study their antibiotic resistance profiles. Methods: We collected data referring to patients hostpitalized for K. pneumoniae infections in the 4 university hospitals of Marseille from January 2012 to July 2015. We then study their antibiotic resistance profiles according the clinical sites from which each strain was collected. Antibiotic consumption data from our four hospitals were also analyzed from January 2013 to July 2015. Results: Overall, 4868 patients were admitted in our settings for K. pneumoniae infections over the study period. Overall, 40.1, 22.3, 25.6, 0.4, 29.9, 14.8, 27.3 and 37.0 % of the strains were resistant to amoxicillin plus clavulanic acid, piperacillin-tazobactam, ceftriaxone, imipenem, ciprofloxacin, gentamicin, trimethoprim-sulfamethoxazole and furan, respectively. 447 were invasive infections. The resistance level of our invasive strains was significantly lower than that presented by 11, 7, 10 and 11 other European countries included in the 2013 European Antimicrobial Resistance Surveillance Network report for ceftriaxone, imipenem, ciprofloxacin and gentamicin, respectively, but significantly higher than that of 13, 1, 17 and 13 European countries for the same antibiotics. We also observed that the percentages of resistance of our invasive strains to three of the four antibiotics decreased over the study. In parallel, antibiotic consumption remained stable in our four hospitals from January 2013 to July 2015. Conclusions: Altogether, our results underline that automated antibiotic-susceptibility testing results-based surveillance systems are crucial to better understand the evolving epidemiology of dangerous pathogenic bacterial species, like K. pneumoniae, at local scales. [ABSTRACT FROM AUTHOR]

Enterococci are gram-positive cocci responsible for various infections worldwide, and their prevalence of antibiotic resistance greatly varies worldwide. This study investigates the prevalence of resistance to antibiotics in enterococci from patients admitted in the four university hospitals of Marseille between January 2013 and September 2014. Two thousand nine hundred seventy-six patients-bacteria couples were identified (2,507 Enterococcus faecalis and 469 Enterococcus faecium) in the four university hospitals of Marseille. 1.3%, 8.9%, 1.4%, and 0% of E. faecalis strains were resistant to amoxicillin, gentamicin, teicoplanin, and vancomycin, respectively, and 83.9%, 49.2%, 1.3%, and 0.2% of E. faecium strains were resistant to amoxicillin, gentamicin, teicoplanin, and vancomycin, respectively. Resistance to aminoglycosides and vancomycin in strains isolated from blood cultures was significantly lower than that of most European countries included in the 2012 European Antimicrobial Resistance Surveillance Network report. Our low percentage of antibiotic resistance in enterococci is likely due to a low level of E. faecium infections, underlining the need to implement surveillance systems, especially to monitor the E. faecalis/ E. faecium ratio evolution in blood cultures and others. [ABSTRACT FROM AUTHOR]

The article discusses aspects of microbiological research and infectious diseases. Topics include the research by the Pasteur Institute which discovered the human immunodeficiency virus, research framework of the University Hospital Institute (IHU) Méditerranée Infection, and a model that integrate all aspects of microbiology with infectious diseases.

The disc diffusion method has long been considered the standard technique for antibiotic susceptibility testing (AST) in clinical microbiology laboratories because of its simplicity, reproducibility and low cost compared with commercial automated microdilution systems that are usually more rapid but less sensitive for detecting important mechanisms of resistance. Here we measured reading zone diameters around antibiotics in a series of 25 well-characterised Gram-negative bacteria by the disc diffusion technique in real-time using an Advencis Bio-System instrument consisting of a real-time high-resolution video imager in a dedicated incubator. The susceptibility of wild-type Gram-negative bacteria to imipenem, determined by reading the diameter of inhibition, was detectable as early as 3.5 h (mean time 3.7 ± 0.45 h), whereas carbapenemase-producing Gram-negative bacteria could be correctly categorised as early as 3 h (mean time 4.2 ± 0.8 h) of incubation. Similarly, the characteristic champagne cork aspect of extended-spectrum β-lactamase (ESBL) could be detected by the system as early as 3.5 h. Moreover, we present here for the first time video movies of the appearance of the diameter of inhibition by disc diffusion in real-time. This preliminary study using a new and innovative technology provides for a renewed interest for microbiologists who wish to continue to use the disc diffusion method as a reference method for AST. New video imaging technology presents a proof of concept that could improve the real-time management of patients with AST within a very rapid turnaround time and can provide a large financial saving for hospitals. [ABSTRACT FROM AUTHOR]

Recently, there has been a steady increase in the number of recognized pathogenic microorganisms, specifically bacteria. The development of genetic technologies, MALDI-TOF mass spectrometry and new culturing techniques has significantly widened the repertoire of known microorganisms and therefore pathogenic microorganisms. The repertoire of infectious agents has been studied in various environments including water, soil, pets, livestock, wildlife and arthropods. Using different methods, many known pathogens can be identified in these samples; therefore, the impact of emergent pathogens on humans can be examined and novel pathogens can be identified. In this special issue, we discuss the identification of emerging pathogens in the environment and animals. [ABSTRACT FROM AUTHOR]

The repertoire of microeukaryotes in the human gut has been poorly explored, mainly in individuals living in northern hemisphere countries. We further explored this repertoire using PCR-sequencing and culture in seven individuals living in four tropical countries. A total of 41 microeukaryotes including 38 different fungal species and three protists were detected. Four fungal species, Davidiella tassiana, Davidiella sp., Corticiaceae sp., and Penicillium sp., were uniquely detected by culture; 27 fungal species were uniquely detected using PCR-sequencing and Candida albicans, Candida glabrata, Trichosporon asahii, Clavispora lusitaniae, Debaryomyces hansenii, Malassezia restricta, and Malassezia sp. were detected using both molecular and culture methods. Fourteen microeukaryotes were shared by the seven individuals, whereas 27 species were found in only one individual, including 11 species in Amazonia, nine species in Polynesia, five species in India, and two species in Senegal. These data support a worldwide distribution of Malassezia sp., Trichosporon sp., and Candida sp. in the gut mycobiome. Here, 13 fungal species and two protists, Stentor roeseli and Vorticella campanula, were observed for first time in the human gut. This study revealed a previously unsuspected diversity in the repertoire of human gut microeukaryotes, suggesting spots for further exploring this repertoire. [ABSTRACT FROM AUTHOR]

In the article, the authors discuss the importance of rickettsioses, particularly among Dutch travelers. Topics include the challenges in diagnosing rickettsioses using serological methods, the use by countries like India of the Weil Felix technique to diagnose the condition, and the top infections affecting U.S. personnel after the Vietnam War, namely, leptospirosis, scrub typhus, and murine typhus.

The article explores the emergence of microbiology in the 19th century which was made possible by the use of new tools, including the popularization of the microscope, development of culture techniques, and the discovery that some bacteria could not be grown in presence of oxygen. The development of techniques of staining and gelification of culture media is noted. It notes research on Bacillus anthracis and Mycobacterium tuberculosis as infectious causative agents of anthrax and tuberculosis.

Abstract: Bartonella spp. are responsible for emerging and re-emerging diseases around the world. The majority of human infections are caused by Bartonella henselae, Bartonella quintana and Bartonella bacilliformis, although other Bartonella spp. have also been associated with clinical manifestations in humans. The severity of Bartonella infection correlates with the patient's immune status. Clinical manifestations can range from benign and self-limited to severe and life-threatening disease. Clinical conditions associated with Bartonella spp. include local lymphadenopathy, bacteraemia, endocarditis, and tissue colonisation resulting in bacillary angiomatosis and peliosis hepatis. Without treatment, Bartonella infection can cause high mortality. To date, no single treatment is effective for all Bartonella-associated diseases. In the absence of systematic reviews, treatment decisions for Bartonella infections are based on case reports that test a limited number of patients. Antibiotics do not significantly affect the cure rate in patients with Bartonella lymphadenopathy. Patients with Bartonella spp. bacteraemia should be treated with gentamicin and doxycycline, but chloramphenicol has been proposed for the treatment of B. bacilliformis bacteraemia. Gentamicin in combination with doxycycline is considered the best treatment regimen for endocarditis, and erythromycin is the first-line antibiotic therapy for the treatment of angioproliferative lesions. Rifampicin or streptomycin can be used to treat verruga peruana. In this review, we present recent data and recommendations related to the treatment of Bartonella infections based on the pathogenicity of Bartonella spp. [Copyright &y& Elsevier]

Mycobacterium tuberculosis culture, a critical technique for routine diagnosis of tuberculosis, takes more than two weeks. Here, step-by-step improvements in the protocol including a new medium, microaerophlic atmosphere or ascorbic-acid supplement and autofluorescence detection dramatically shortened this delay. In the best case, primary culture and rifampicin susceptibility testing were achieved in 72 hours when specimens were inoculated directly on the medium supplemented by antibiotic at the beginning of the culture. [ABSTRACT FROM AUTHOR]

Background Few studies have focused on eukaryote community in the human gut. Here, the diversity of microeukaryotes in the gut microbiota of an anorexic patient was investigated using molecular and culture approaches. Case presentation A 21-year-old Caucasian woman was admitted in an intensive care unit for severe malnutrition in anorexia nervosa. One stool specimen was collected from the anorexic patient, culture and polymerase chain reaction-based explorations yielded a restricted diversity of fungi but four microeukaryotes Tetratrichomonas sp., Aspergillus ruber Penicillium solitum and Cladosporium bruhnei previously undescribed in the human gut. Conclusions Establishing microeukaryote repertoire in gut microbiota contributes to the understanding of its role in human health. [ABSTRACT FROM AUTHOR]

Microbes were defined in the 19th century by L. Pasteur. Prokaryotes and eukaryotes, which are divided into two worlds of microbes, were introduced by E. Chatton in 1925. R. Woese divided this world into three domains based on ribosomal analysis (Bacteria, Archaea, and Eukarya). The discovery of Mimivirus and other Megavirales, that are microbes, led to divide the microbiological world into four branches. I introduced the name TRUC (Things Resisting Uncompleted Classifications) to accommodate the division in four of the currently known microbiological world. © 2013 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Abstract: Hybridization is increasingly seen as an important source of adaptive genetic variation and biotic diversity. Recent phylogenetic studies on the early evolution of birds suggest that the early diversification of neoavian orders perhaps involved a period of extensive hybridization or incomplete lineage sorting. Phylogenetic error, saturation, long-branch attraction, and convergence make it difficult to detect ancient hybridization events and differentiate them from incomplete lineage sorting using sequence data. We used recently published retroposon marker data to visualize the early radiation of Neoaves within a phylogenetic network approach, and found that the most basal neoavian taxa indeed show a complex pattern of reticulated relationships. Moreover, the reticulation levels of different parts of the network are consistent with the insertion pattern of the retroposon elements. The use of network-based analyses on homoplasy-free data shows true conflicting signals and the taxa involved that are not represented in trees. [Copyright &y& Elsevier]

• SARS-CoV-2. • Seroprevalence. • Performing serology retrospectively. • How to evaluate the extent of the epidemics. [ABSTRACT FROM AUTHOR]

Background: Recent advances of genomics and metagenomics reveal remarkable diversity of viruses and other selfish genetic elements. In particular, giant viruses have been shown to possess their own mobilomes that include virophages, small viruses that parasitize on giant viruses of the Mimiviridae family, and transpovirons, distinct linear plasmids. One of the virophages known as the Mavirus, a parasite of the giant Cafeteria roenbergensis virus, shares several genes with large eukaryotic self-replicating transposon of the Polinton (Maverick) family, and it has been proposed that the polintons evolved from a Mavirus-like ancestor. Results: We performed a comprehensive phylogenomic analysis of the available genomes of virophages and traced the evolutionary connections between the virophages and other selfish genetic elements. The comparison of the gene composition and genome organization of the virophages reveals 6 conserved, core genes that are organized in partially conserved arrays. Phylogenetic analysis of those core virophage genes, for which a sufficient diversity of homologs outside the virophages was detected, including the maturation protease and the packaging ATPase, supports the monophyly of the virophages. The results of this analysis appear incompatible with the origin of polintons from a Mavirus-like agent but rather suggest that Mavirus evolved through recombination between a polinton and an unknownvirus. Altogether, virophages, polintons, a distinct Tetrahymena transposable element Tlr1, transpovirons, adenoviruses, and some bacteriophages form a network of evolutionary relationships that is held together by overlapping sets of shared genes and appears to represent a distinct module in the vast total network of viruses and mobile elements. Conclusions: The results of the phylogenomic analysis of the virophages and related genetic elements are compatible with the concept of network-like evolution of the virus world and emphasize multiple evolutionary connections between bona fide viruses and other classes of capsid-less mobile elements. [ABSTRACT FROM AUTHOR]

Background: Methanobrevibacter smithii, Methanobrevibacter oralis, Methanosphaera stadtmanae, Methanomassilicoccus luminyensis and Methanobrevibacter arboriphilicus have been cultured from human digestive microbiota. Each one of these fastidious methanogenic archaea requires a specific medium for its growth, hampering their routine isolation and the culture. Methodology/Principal Findings: A new culture medium here referred as SAB medium was optimized and tested to cultivate methanogens associated with human microbiota, as well as two mesophile methanogens Methanobacterium beijingense and Methanosaeta concilii. It was further tested for the isolation of archaea from 20 human stool specimens including 10 specimens testing positive for PCR detection of M. smithii. After inoculating 105 colony-forming-unit archaea/mL or 1 g stool specimen in parallel in SAB medium and reference DSMZ medium in the presence of negative controls, growth of archaea was determined by optical microscopy and the measurement of methane production by gas chromatography. While the negative controls remained sterile, all tested archaea grew significantly more rapidly in SAB medium than in reference medium in 1–3 days (P<0.05, Student test). Among PCR-positive stool specimens, 10/10 grew in the SAB medium, 6/10 in DSMZ 119 medium, 5/10 in DSMZ 322 medium and 3/10 in DSMZ 334 c medium. Four out of ten PCR-negative stool specimens grew after a 3-week incubation in the SAB-medium whereas no growth was detected in any of the reference media. 16S rRNA gene sequencing yielded 99–100% sequence similarity with reference M. smithii except for one specimen that yielded 99–100% sequence similarity with reference Methanobrevibacter millerae. Conclusions/Significance: SAB medium allows for the versatile isolation and growth of methanogenic archaea associated with human gut microbiota including the archaea missed by inoculation of reference media. Implementation of the SAB medium in veterinary and medical microbiology laboratories will ease the routine culture-based detection of methanogenic archaea in clinical and environmental specimens. [ABSTRACT FROM AUTHOR]

Background: Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient. Methodology/Principal Findings: A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants. Conclusions/Significance: Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health. [ABSTRACT FROM AUTHOR]

Head lice and body lice have distinct ecologies and differ slightly in morphology and biology, questioning their taxonomic status. Over the past 10 years many genetic studies have been undertaken. Controversial data suggest that not only body lice but also head lice can serve as vectors of Bartonella quintana, and a better understanding of louse epidemiology is crucial. Here, we review taxonomic studies based on biology and genetics, including genomic data on lice, lice endosymbionts, and louse-transmitted bacteria. We recommend that studies of human lice employ morphological and biological characteristics in conjunction with transcriptomic date because lice seem to differ mainly in gene expression (and not in gene content), leading to different phenotypes. [ABSTRACT FROM AUTHOR]

Dridi B, Raoult D, Drancourt M. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of Archaea: towards the universal identification of living organisms. APMIS 2012; 120: 85-91. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) identification of Archaea has been limited to some environmental extremophiles belonging to distant taxa. We developed a specific protocol for MALDI-TOF-MS identification of Archaea and applied it to seven environmental human-associated Methanobrevibacter smithii, Methanobrevibacter oralis, Methanosphaera stadtmanae, and the recently described Methanomassiliicoccus luminyensi Archaea. After mechanical lyse, we observed a unique protein profile for each organisms comprising 7-24 peaks ranging from 3 015 to 10 632 Da with a high quality score of 7.38 ± 1.26. Profiles were reproducible over successive experiments performed at 1, 2, and 3-week growth durations and unambiguously distinguished the Archaea from all of the 3 995 bacterial spectra in the Brüker database. After the incorporation of the determined profiles into a local database, archaeal isolates were blindly identified within 10 min with an identification score of 1.9-2.3. The MALDI-TOF-MS-based clustering of these archaeal organisms was consistent with their 16S rDNA sequence-based phylogeny. These data prove that MALDI-TOF-MS profiling could be used as a first-line technique for the identification of human Archaea. In complement to previous reports for animal cells, Bacteria and giant viruses, MALDI-TOF-MS therefore appears as a universal method for the identification of living unicellular and multicellular organisms. [ABSTRACT FROM AUTHOR]

Summary: Genome-scale analysis suggests that the last common ancestor of the Mycobacterium tuberculosis complex and Mycobacterium leprae diverged 36 million years ago, and members of the Mycobacterium tuberculosis complex differentiated 40 000 years ago. Analysis of palaeomicrobiological data from a 17 000-year-old sample from a bison and a 9000-year-old sample from a human being suggested that M tuberculosis preceded Mycobacterium bovis and related species. Whole-genome comparisons show that members of the M tuberculosis complex form a unique bacterial species with distinct ecotypes that are transmissible from any infected mammalian species to several others. Genomic deletions identified several M tuberculosis lineages that could be placed on a phylogeographical map, suggesting adaptation to local host populations. The degrees of transmissibility and virulence vary between M tuberculosis clones, with increased virulence mainly linked to gene loss in regulatory pathways. Such data suggest that most M tuberculosis clones have a restricted spreading capacity between the host population, allowing unpredictable bursts of highly transmissible, virulent, and successful clones, such as the east Asian (Beijing) clone. Advances in genomics have helped the development of molecular techniques for accurate identification of species and clones in the M tuberculosis complex, which is essential for tracing the source of infections. [ABSTRACT FROM AUTHOR]

Immuno-PCR (iPCR) is a method that combines the advantages of both enzyme-linked immunosorbent assay and PCR and is a powerful method for detecting low quantities of protein antigens. Despite its potential, for a long time iPCR was an underutilized method as evidenced by the low number of publications on its routine application. The introduction of ready-to-use reagents, the large choice in linker molecule, reduction of protocol time and the development of new systems is opening the way for iPCR to become a routine method for use as a microbial diagnostic. To understand how iPCR could become an indispensible microbial diagnostic, we review the evolution of iPCR, from its first classical format with numerous drawbacks to more sophisticated systems developed to circumvent these drawbacks. [Copyright &y& Elsevier]

Rickettsia are best known as strictly intracellular vector-borne bacteria that cause mild to severe diseases in humans and other animals. Recent advances in molecular tools and biological experiments have unveiled a wide diversity of Rickettsia spp. that include species with a broad host range and some species that act as endosymbiotic associates. Molecular phylogenies of Rickettsia spp. contain some ambiguities, such as the position of R. canadensis and relationships within the spotted fever group. In the modern era of genomics, with an ever-increasing number of sequenced genomes, there is enhanced interest in the use of whole-genome sequences to understand pathogenesis and assess evolutionary relationships among rickettsial species. Rickettsia have small genomes (1.1-1.5 Mb) as a result of reductive evolution. These genomes contain split genes, gene remnants and pseudogenes that, owing to the colinearity of some rickettsial genomes, may represent different steps of the genome degradation process. Genomics reveal extreme genome reduction and massive gene loss in highly vertebrate-pathogenic Rickettsia compared to less virulent or endosymbiotic species. Information gleaned from rickettsial genomics challenges traditional concepts of pathogenesis that focused primarily on the acquisition of virulence factors. Another intriguing phenomenon about the reduced rickettsial genomes concerns the large fraction of non-coding DNA and possible functionality of these 'non-coding' sequences, because of the high conservation of these regions. Despite genome streamlining, Rickettsia spp. contain gene families, selfish DNA, repeat palindromic elements and genes encoding eukaryotic-like motifs. These features participate in sequence and functional diversity and may play a crucial role in adaptation to the host cell and pathogenesis. Genome analyses have identified a large fraction of mobile genetic elements, including plasmids, suggesting the possibility of lateral gene transfer in these intracellular bacteria. Phylogenetic analyses have identified several candidates for horizontal gene acquisition among Rickettsia spp. including tra, pat2, and genes encoding for the type IV secretion system and ATP/ADP translocase that may have been acquired from bacteria living in amoebae. Gene loss, gene duplication, DNA repeats and lateral gene transfer all have shaped rickettsial genome evolution. A comprehensive analysis of the entire genome, including genes and non-coding DNA, will help to unlock the mysteries of rickettsial evolution and pathogenesis. [ABSTRACT FROM AUTHOR]

Abstract: In this work, we review the state of knowledge of Archaea associated with the human microbiome. These prokaryotes, initially discovered in extreme environments, were named Archaea because these environments were thought to be the most primitive on Earth. Further research revealed that this terminology is misleading because these organisms were later found in various non-extreme environments, including the human host. Further examination of the human microbiome has enabled the isolation of three archaeal species, Methanobrevibacter smithii, Methanosphaera stadtmanae and Methanobrevibacter oralis, which are associated with oral, intestinal and vaginal mucosae in humans. Moreover, molecular studies including metagenomic analyses detected DNA sequences indicative of the presence of additional methanogenic and non-methanogenic Archaea in the human intestinal tract. All three culturable Archaea are strict anaerobes, although their potential role in human diseases remains to be established. Future research aims to detect and culture additional human mucosa-associated Archaea and to look for their presence in additional human tissues, to establish their role in human infections involving complex flora. [Copyright &y& Elsevier]

Background: We conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans (''bad bugs'') to their closest non-epidemic related species (''controls''). Methodology/Principal Findings: We found several significantly different features in the ''bad bugs'', one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG) functional categories revealed a significantly smaller number of genes in the ''bad bugs'', which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five ''bad bugs'' showed a greater number of poly (A) tails compared to the controls, whereas an elevated number of poly (A) tails was found to be strongly correlated to a low GC% content. The ''bad bugs'' had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA) showed that the ''bad bugs'' had surprisingly more toxin-antitoxin modules than did the controls. Conclusions/Significance: We conclude that pathogenic capacity is not the result of ''virulence factors'' but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution. [ABSTRACT FROM AUTHOR]

Summary We have developed a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based identification technique for Planctomycetes organisms, which are used here as bacteria of suitable diversity at genus and species level for testing resolution of the method. Planctomyces maris ATCC 29201, Planctomyces brasiliensis ATCC 49424T, P. brasiliensis ATCC 49425, Planctomyces limnophilus ATCC 43296T, Blastopirellula marina ATCC 49069T, Rhodopirellula baltica DSM 10527T and Gemmata obscuriglobus DSM 5831T were cultured on half-strength marine broth and agar, or alternatively on caulobacter broth and agar. The resulting pellets of organisms (liquid) or colonies (solid agar) were directly applied to a MALDI-TOF plate. This yielded a reproducible, unique protein profiles comprising 23-39 peaks ranging in size from 2403 to 12 091 Da. These peaks were unambiguously distinguished from any of the 3038 bacterial spectra in the Brüker database. Matrix-assisted laser desorption/ionization time-of-flight patterns were similar for isolates grown in solid and in liquid medium, albeit the patterns from solid growth were more easily interpretable. After the incorporation of the herein determined profiles into the Brüker database, Planctomycetes isolates were blindly identified within 10 min, with an identification score in the range of 1.8 to 2.3. Matrix-assisted laser desorption/ionization time-of-flight-based clustering of these Planctomycetes organisms was consistent with 16S rDNA-based phylogeny. However, the incorporation of additional non- Planctomycetes MALDI-TOF profiles in the analysis resulted in inconsequential clustering. In conclusion, MALDI-TOF protein profiling is a new approach for the rapid and accurate identification of cultured environmental organisms, as illustrated in this study through the analysis of Planctomycetes. [ABSTRACT FROM AUTHOR]

Acanthamoeba polyphaga mimivirus, Marseillevirus, and Sputnik, a virophage, are intra-amoebal viruses that have been isolated from water collected in cooling towers. They have provided fascinating data and have raised exciting questions about viruses definition and evolution. Mimivirus and Marseillevirus have been classified in the nucleo-cytoplasmic large DNA viruses (NCLDVs) class. Their genomes are the largest and fifth largest viral genomes sequenced so far. The gene repertoire of these amoeba-associated viruses can be divided into four groups: the core genome, genes acquired by lateral gene transfer, duplicated genes, and ORFans. Open reading frames (ORFs) that have homologs in the NCLDVs core gene set represent 2.9 and 6.1% of the Mimivirus and Marseillevirus gene contents, respectively. A substantial proportion of the Mimivirus, Marseillevirus and Sputnik ORFs exhibit sequence similarities to homologs found in bacteria, archaea, eukaryotes or viruses. The large amount of chimeric genes in these viral genomes might have resulted from acquisitions by lateral gene transfers, implicating sympatric bacteria and viruses with an intra-amoebal lifestyle. In addition, lineage-specific gene expansion may have played a major role in the genome shaping. Altogether, the data so far accumulated on amoeba-associated giant viruses are a powerful incentive to isolate and study additional strains to gain better understanding of their pangenome. Copyright © 2010 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Amoebae are unicellular phagocytes that feed on microorganisms in their environment. Some amoebae have the largest genome size currently known on earth. They phagocytose any inert particle larger than 0.5 μm. Phagocytic amoebae can harbor different bacteria, fungi and giant viruses within the same cell. There is evidence of lateral gene transfer between the amoeba and its microbiological hosts. There is also evidence of gene exchange between viruses and bacteria hosted in amoebae. Moreover, there is evidence of gene transfer between viruses, such as Mimivirus and the virophage. As a consequence, viruses and intracellular bacteria living in amoebae have a sympatric lifestyle and large chimeric genome repertoires. We conclude that phagocytic protists continuously generate new species with chimeric repertoires that may succeed later if adapted to the environmental conditions and selected in a specific niche. Copyright © 2010 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Abstract: Obligate intracellular bacteria are privileged soldiers on the battlefield that represent host–pathogen interactions. Microarrays are a powerful technology that can increase our knowledge about how bacteria respond to and interact with their hosts. This review summarizes the limitations inherent to host–pathogen interaction studies and essential strategies to improve microarray investigations of intracellular bacteria. We have compiled the comparative genomic and gene expression analyses of obligate intracellular bacteria currently available from microarrays. In this review we explore ways in which microarrays can be used to identify polymorphisms in different obligate intracellular bacteria such as Coxiella burnetii, Chlamydia trachomatis, Ehrlichia chaffeensis, Rickettsia prowazekii and Tropheryma whipplei. These microarray studies reveal that, while genomic content is highly conserved in obligate intracellular bacteria, genetic polymorphisms can potentially occur to increase bacterial pathogenesis. Additionally, changes in the gene expression of C. trachomatis throughout its life cycle, as well as changes in the gene expression profile of the pathogens R. prowazekii, Rickettsia rickettsii, Rickettsia typhi, T. whipplei and C. trachomatis following environmental changes, are discussed. Finally, an in vivo model of Rickettsia conorii within the skin is discussed. The gene expression analyses highlight the capacity of obligate intracellular bacteria to adapt to environmental changes and potentially to thwart the host response. [Copyright &y& Elsevier]

Background: A bacterial role in the obesity pandemic has been suspected based on the ingestion of probiotics that can modify the gut flora. The objective of our study was to determine if increased Lactobacillus sp. in the gut flora of newborn broiler chicks and ducks could result in weight gain increase. Methodology: Female broiler chicks (Gallus gallus domesticus) and ducks (Anas platyrhynchos domestica) were separated into one control and two experimental groups, and inoculated once or twice with 4x1010 Lactobacillus spp. per animal in PBS, or with PBS alone. Fecal samples were collected before and at 24 hours, 2, 4, 8, 16 and 30 days after the inoculation. DNA was extracted from the stools, and qPCR assays were performed on a MX3000TM system for the detection and quantification of Lactobacillus sp., Bacteroidetes and Firmicutes, using a quantification plasmid. Animals were measured and sacrificed 60 days after the beginning of the experiment, and livers were collected and measured. Principal Findings: Chicks inoculated once and twice with Lactobacillus weighed 10.2% (p = 0.0162) and 13.5% (p = 0.0064) more than the control group animals, respectively. Similarly, ducks inoculated once and twice weighed 7.7% (p = 0.05) and 14% (p = 0.035) more than those in the control group, respectively. Liver mass was also significantly higher in inoculated animals compared to the control group. Inoculation with Lactobacillus sp. increased the DNA copies of Lactobacillus spp. and Firmicutes in the stools. Bacteroidetes remained stable, and only the second Lactobacillus sp. inoculation significantly decreased its population in chicks. The ratio of DNA copies of Firmicutes to those of Bacteroidetes increased to as much as 6,4 in chicks and 8,3 in ducks. Conclusions: Differences in the intestinal microbiota may precede weight increase, as we found that an increase of Lactobacillus sp. in newborn ducks and chicks preceded the development of weight gain. [ABSTRACT FROM AUTHOR]

Tropheryma whipplei, which causes Whipple disease, is found in human feces and may cause gastroenteritis. To show that T. whipplei causes gastroenteritis, PCRs for T. whipplei were conducted with feces from children 2-4 years of age. Western blotting was performed for samples from children with diarrhea who had positive or negative results for T. whipplei. T. whipplei was found in samples from 36 (15%) of 241 children with gastroenteritis and associated with other diarrheal pathogens in 13 (33%) of 36. No positive specimen was detected for controls of the same age (0/47; p = 0.008). Bacterial loads in case-patients were as high as those in patients with Whipple disease and significantly higher than those in adult asymptomatic carriers (p = 0.002). High incidence in patients and evidence of clonal circulation suggests that some cases of gastroenteritis are caused or exacerbated by T. whipplei, which may be co-transmitted with other intestinal pathogens. [ABSTRACT FROM AUTHOR]

Bartonella quintana is a re-emerging pathogen and the causative agent of a variety of disease manifestations in humans including trench fever. Various typing methods have been developed for B. quintana, but these tend to be limited by poor resolution and, in the case of gel-based methods, a lack of portability. Multilocus sequence typing (MLST) has been used to study the molecular epidemiology of a large number of pathogens, including B. henselae, a close relative of B. quintana. We developed a MLST scheme for B. quintana based on the 7 MLST loci employed for B. henselae with two additional loci to cover underrepresented regions of the B. quintana chromosome. A total of 16 B. quintana isolates spanning over 60 years and three continents were characterized. Allelic variation was detected in five of the nine loci. Although only 8/4270 (0.002%) of the nucleotide sites examined were variable over all loci, these polymorphisms resolved the 16 isolates into seven sequence types (STs). We also demonstrate that MLST can be applied on uncultured isolates by direct PCR from cardiac valve tissue, and suggest this method presents a promising approach for epidemiological studies in this highly clonal organism. Phylogenetic and clustering analyses suggest that two of the seven STs form a distinct lineage within the population. [ABSTRACT FROM AUTHOR]

Abstract: Q fever is a zoonotic disease caused by the ubiquitous pathogen Coxiella burnetii responsible for acute and chronic clinical manifestations. Farm animals and pets are the main reservoirs of infection, and transmission to human beings is mainly accomplished through inhalation of contaminated aerosols. This illness is associated with a wide clinical spectrum, from asymptomatic or mildly symptomatic seroconversion to fatal disease. In humans Q fever can manifest as an acute disease (mainly as a self-limited febrile illness, pneumonia, or hepatitis) or as a chronic disease (mainly endocarditis), especially in patients with previous valvulopathy and to a lesser extent in immunocompromised hosts and in pregnant women. In contrast in animals, Q fever is in most cases, strikingly asymptomatic. The definite diagnosis of Q fever is made based on a significant increase in serum antibody titers, the determination of which often requires considerable time, and therefore patients must be monitored for a certain period. The treatment is effective and well tolerated, but must be adapted to the acute or chronic pattern with the tetracyclines to be considered the mainstay of antibiotic therapy. Several actions have been proposed to prevent and reduce the animal and environmental contamination. Vaccination of animals in infected flocks, as well as in uninfected ones close to them, with an efficient vaccine can prevent abortions and shedding of the bacteria. [Copyright &y& Elsevier]