Yersinia pestis: the Natural History of Plague.

The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

Taxono-genomics and description of Haloimpatiens massiliensis sp. nov., a new bacterium isolated from the gut of a healthy infant.

A polyphasic taxono-genomic strategy was used to describe a new bacterium, strain Marseille-P1935; isolated from the gut of a healthy infant. 16S rRNA sequencing showed that the isolate belongs to the genus Haloimpatiens in the family Clostridiaceae. Phenotypic analysis and whole-genome sequence analyses confirm the status of the new species. We propose the creation of the new species Haloimpatiens massiliensis strain Marseille-P1935T (= CSURP1935T; = DSM100591T).

Anaerotruncus massiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery.

A new bacterium, strain AT3T, was isolated by microbial culturomics from a faecal sample from a Frenchman after bariatric surgery. The isolate exhibited 96.6% 16S ribosomal RNA gene nucleotide sequence similarity with Anaerotruncus colihominis strain WAL 14565T = CCUG 45055T = CIP 107754T. Phenotypic and genomic characteristics showed that the new strain represents a novel species, for which the name Anaerotruncus massiliensis sp. nov. is proposed. The type strain is strain AT3T = CSUR P2007T = DSM 100567T.

Management of patients presenting with generalized musculoskeletal pain and a suspicion of Lyme disease.

Lyme disease is caused by bacteria of the B. burgdorferi sensu lato complex, and can give polymorphic clinical manifestations that can affect several organs such as the skin, the central nervous system, or the joints. In recent years, patients' associations and physicians have been supporting the hypothesis that this infection would manifest as chronic generalized musculoskeletal pain symptoms, named "chronic Lyme disease". Fibromyalgia is a clinical presentation characterized by chronic generalized musculoskeletal pain with a major impact on quality of life and social and psychological functioning. We analyzed existing literature data on pain syndromes associated with Lyme disease (post-treatment Lyme disease syndrome) or tick bites (polymorphic symptoms after a tick bite). We also analyzed existing data on the diagnosis, pathophysiology, and treatment of fibromyalgia. Our review shows that post-treatment Lyme disease syndrome has characteristics very close to post-infectious fibromyalgia. On the other hand, patients presenting for Lyme disease screening because of chronic generalized musculoskeletal pain symptoms after a tick bite should also be screened for fibromyalgia to allow appropriate management. Antibiotics are not recommended here.

Functional neuroimaging in patients presenting with somatoform disorders: A model for investigating persisting symptoms after tick bites and post-treatment Lyme disease syndrome?

Approximately 10% of patients presenting with Lyme disease experience fatigue, musculoskeletal pain, concentration disorders, or short-term memory deficits in the six months following treatment. This entity has been defined as post-Lyme disease syndrome or post-treatment Lyme disease syndrome. The pathophysiology of this syndrome is unknown, but neither persistence of the bacterium nor effectiveness of antibiotics are currently reported in the literature. The French High Council for Public Health (French acronym HCSP) has recently defined a new entity called "persistent polymorphic symptoms after a tick bite" allowing for designing studies to better understand these subjective presentations, for which objective biomarkers are currently lacking. This entity encompasses patients experiencing fatigue and generalized pain in the months following a tick bite and can be associated with several subjective symptoms with major impact on the quality of life. In the field of somatoform disorders, this article reviews functional neuroimaging studies in patients presenting with subjective complaints and discusses potential clinical implications for persisting symptoms after tick bites and post-treatment Lyme disease syndrome.

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.

Peptoniphilus lacydonensis sp. nov., a new human-associated species isolated from a patient with chronic refractory sinusitis.

Strain EL1T was isolated from a sinus sample of an 85-year-old man with chronic refractory sinusitis complicating ethmoidal adenocarcinoma. We studied its phenotypic and genomic characteristics. This is a Gram stain-positive, anaerobic and microaerophilic coccus. Cells are catalase negative, nonmotile and non-spore forming. The major fatty acids are saturated hexadecanoic acid (34%), unsaturated 9-octadecenoic acid (32%) and 9.12-octadecadienoic acid (21%). The 1.86 Mb long genome exhibits a 29.9% G+C content and contains 1750 protein-coding and 43 RNA genes. On the basis of these data, we propose the creation of the new human-associated bacterial species Peptoniphilus lacydonensis sp. nov.

Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon.

Strain Marseille-P2645T was isolated in a colon sample from a Frenchwoman who underwent a colonoscopy. Bacterial cells were Gram negative, non-spore forming, mobile and strictly anaerobic. The genome of strain Marseille-P2645T is 3 950 441 bp long and contains 3374 protein-coding genes. The DNA G+C content is of 51.66 mol%. Strain Marseille-P2645T exhibited a 92.9% sequence similarity with Bacteroides helcogenes strain P36-108T (GenBank accession no. CP002352), the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2645T (= CSUR P2645 = DSM 103034) is therefore a candidate as a type species of a new genus belonging to the Bacteroidaceae family, for which the name of Mediterranea massiliensis gen. nov., sp. nov., is proposed.

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.

Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman.

Massilioclostridium coli strain Marseille-P2976T (= CSUR P2976 = DSM 103344) is a new bacterial genus isolated from the left colon of a patient who underwent colonoscopy for colorectal cancer screening. Massilioclostridium coli is a Gram-negative bacillus, strict anaerobic, nonsporogenous and nonmotile organism. We describe here the strain Marseille-P2976T and provide its complete annotated genome sequence according to taxonogenomics concepts. Its genome is 2 985 330 bp long and contains 2562 predicted genes and 75 RNA genes.

Recombinant expression of Mimivirus L725 ORFan gene product.

Mimivirus was the first discovered amoebal giant virus. The Mimivirus virions are covered by a dense layer of approximately 130 nm-long fibers, the length and shape of which diverge from those of other viruses. Here, we aimed at expressing the L725 protein to further confirm and study its role as a fiber-associated protein. We report Escherichia coli expression of the L725 protein, which is encoded by a Mimivirus ORFan, was previously identified by proteomics in purified viral fibers and demonstrated to be a fiber-associated protein by RNA-silencing experiments. The expressed protein was recognized by anti-Mimivirus fiber or anti-Mimivirus L725 polyclonal antibodies. This study is the only expression, to our knowledge, of a product from a Mimiviral ORFan gene.

"Anaerotruncus massiliensis," a new species identified from human stool from an obese patient after bariatric surgery.

We report the main characteristics of a new bacterial species strain AT3T (CSUR = P2007, DSM = 100567) that was isolated from the stool sample collected from a 47-year-old obese French man after he underwent bariatric surgery.

"Ruminococcus phoceensis," a new species identified from human stool from an obese patient before bariatric surgery.

We report here the main characteristics of a new bacterium species, "Ruminococcus phoceensis" strain AT10 (CSUR = P2086, DSM = 100837). This bacterium was isolated from the faeces of a 37-year-old woman from Marseille, France, with morbid obesity before bariatric surgery.

'Eisenbergiella massiliensis', a new species isolated from human stool collected after bariatric surgery.

We report the principal characteristics of 'Eisenbergiella massiliensis' sp. nov. strain AT11 (CSURP = P2120, DSM = 101499) that was isolated from a stool sample collected after bariatric surgery of a 56-year-old obese French woman.

'Negativicoccus massiliensis', a new species identified from human stool from an obese patient after bariatric surgery.

We report here the main characteristics of 'Negativicoccus massiliensis' strain AT7 (CSURP = P2082, DSM = 100853) isolated from a stool sample collected from a 47-year-old obese French man before bariatric surgery.

Tropheryma whipplei DNA in bronchoalveolar lavage samples: a case control study.

Tropheryma whipplei, the causative bacterium of Whipple's disease, can cause acute pneumonia. We performed a case-control study including patients with T. whipplei in bronchoalveolar lavages (BALs) and controls in order to compare patients' clinical statuses. We tested T. whipplei PCR from January 2013 to December 2014, in all the 1438 BALs in Marseille, France. Controls were hospitalized in the same unit during the same period and were comparable in age and sex. Eighty-eight BALs (6.1%) were positive for T. whipplei and 58 patients had pneumonia. Sixty-four patients were male with a mean age of 50.5 years. T. whipplei was commonly associated with aspiration pneumonia (18/88 patients compared with 6/88 controls, p 0.01) and was detected as a unique pathogen in nine cases. Overall, no difference was observed regarding immunocompromised status. Nevertheless, the six AIDS-infected patients in the T. whipplei group had a significantly lower CD4 level than the five AIDS-infected patients in the control group (49 vs. 320/mm3, p 0.01); in addition, five patients were treated with tumour necrosis factor alpha inhibitors (including three treated by monocolonal antibodies and two with soluble receptor) compared with none of the controls (p 0.03). Pneumocystis jirovecii was frequently associated with the T. whipplei group (7/88 vs. 0/88 in control group), Pseudomonas aeruginosa was only detected in the control group (8/88). This study adds evidence for a causative role of T. whipplei in pneumonia. In the future, an experimental model of pneumonia induced by T. whipplei will prove its role in pneumonia.

"Bariatricus massiliensis" as a new bacterial species from human gut microbiota.

We report here the main phenotypic characteristics of "Bariatricus massiliensis" strain AT12 (CSUR P2179), isolated from the stool of a 58-year-old woman who underwent bariatric surgery.

Romboutsia timonensis, a new species isolated from human gut.

The exploration of the human microbiome was recently revolutionized by microbial culturomics and taxonogenomics. Thanks to this approach, we report here the main characteristics of Romboutsia timonensis strain Marseille-P326, a new bacterium isolated from the right human colon by colonoscopy in a 63-year-old French man with severe anaemia with melaena.

Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov.

Strain FF10(T) (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10(T). Results support strain FF10(T) being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov.