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).

Mediastinitis in the intensive care unit patient: a narrative review.

BACKGROUND: Mediastinitis is a rare but severe infection, defined as an inflammation of the connective tissues and structures within the mediastinum. Due to its proximity to vital structures, mediastinitis represents a highly morbid pathological process associated with a high risk of mortality. In most cases mediastinitis requires treatment in the intensive care unit. OBJECTIVES: To highlight to the reader the clinical features of mediastinitis, to attempt to define each clinical scenario, to describe the responsible pathogens and finally to depict both the medical and surgical treatments. SOURCES: We performed a literature search of the PubMed and Cochrane libraries, limited for articles published between January 2003 and December 2018, reporting on acute mediastinitis. CONTENT: The term covers different entities of different aetiologies including deep sternal wound infection related to sternotomy; oesophageal perforation or anastomosis leakage; and finally descending necrotizing mediastinitis, often secondary to oropharyngeal abscess. The responsible pathogens and therefore subsequent management depends on the underlying aetiology. Empirical antimicrobial therapy should cover the suspected microorganisms while surgery and supportive measures should aim to reduce the inoculum of pathogens by providing adequate drainage and debridement. IMPLICATIONS: Literature concerning mediastinitis in the intensive care unit is relatively scarce. We have collated the evidence and reviewed the different causes and treatment options of acute mediastinitis with a particular focus on microbiological epidemiology. Future research in larger cohorts is needed to better understand the treatment of this difficult disease.

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.

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.

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.

"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.

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.

High-quality genome sequence and description of Chryseobacterium senegalense sp. nov.

Strain FF12(T) was isolated from the mouth of a West African lungfish (Protopterus annectens) in Senegal. MALDI-TOF-MS did not provide any identification. This strain exhibited a 97.97% 16S rRNA sequence identity with Kaistella flava. Using a polyphasic study including phenotypic and genomic analyses, strain FF12(T) is Gram-negative, aero-anaerobic, oxidase-positive, non-motile, non-spore-forming, and exhibited a genome of 4,397,629 bp with a G+C content of 35.1% that coded 4,001 protein-coding and 55 RNA genes. On the basis of these data, we propose the creation of Chryseobacterium senegalense strain FF12(T).

High-quality genome sequence and description of Paenibacillus dakarensis sp. nov.

Strain FF9T was isolated in Dakar (Senegal) from a blood-culture taken from a 16-month-old child. MALDI-TOF analysis did not allow for identification. After sequencing, strain FF9T exhibited 98.18% similarity with the 16SrRNA sequence of Paenibacillus uliginis. A polyphasic study of phenotypic and genomic analyses showed that strain FF9T is Gram variable, catalase-positive, and presents a genome of 4,569,428 bp (one chromosome but no plasmid) with 4,427genes (4,352 protein-coding and 75 RNA genes (including 3 rRNA operons). The G+C content is 45.7%. On the basis of these genomic and phenotypic data analyses, we propose the creation of Paenibacillus dakarensis strain FF9T.

Diagnostic performance of [(18)F]fluorodeoxyglucose positron emission tomography-computed tomography in cyst infection in patients with autosomal dominant polycystic kidney disease.

Cyst infection is a common complication of autosomal dominant polycystic kidney disease (ADPKD). Diagnosis is challenging with standard imaging techniques. We aimed to evaluate the diagnostic performance of [(18)F]fluorodeoxyglucose positron emission tomography-computed tomography (18-FDG PET-CT) for the diagnosis of cyst infections among ADPKD patients, in comparison with computed tomography (CT) and magnetic resonance imaging (MRI). All APKD patients who underwent 18-FDG PET-CT for suspected cyst infection between 2006 and 2013 in a French teaching hospital were included. Diagnosis of cyst infection was retained a posteriori on an index of clinical suspicion. 18-FDG PET-CT findings were was considered to be positive in cases of cyst wall hypermetabolism. CT or MRI findings were were considered to be positive in cases of cyst wall thickening (and enhancement if contrast medium was injected) and infiltration of the adjacent fat. A control group of ADPKD patients with 18-FDG PET-CT performed for other reasons was included. Thirty-two 18-FDG PET-CT scans were performed in 24 ADPKD patients with suspected cyst infection. A diagnosis of cyst infection was retained in 18 of 32 cases: 14 with positive 18-FDG PET-CT findings, and four false negatives. There were no false positives and no hypermetabolism of cyst walls in nine ADPKD control patients. 18-FDG PET-CT had a sensitivity of 77%, a specificity of 100%, and a negative predictive value of 77%. 18-FDG PET-CT allowed a differential diagnosis in three patients. In contrast, CT had a sensitivity of 7% and a negative predictive value of 35% (p <0.001 vs. 18-FDG PET-CT). Only eight MRI scans were performed. The diagnostic performance of 18-FDG PET-CT is superior to that of CT in cyst infections, for comparable radiation doses and with no injection of nephrotoxic contrast medium, in ADPKD patients.

Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov.

Strain FF8(T) (= CSUR P860 = DSM 28259) was isolated in Dakar, Senegal, from the urine of a 65-year-old man with acute cystitis. This strain shows a similarity of sequence of 16S rRNA of 98.38% with Weeksella virosa, and its GenBank accession numbers are HG931340 and CCMH00000000. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. Using a polyphasic study made of phenotypic and genomic analyses, strain FF8(T) was a Gram-negative, aerobic rod and a member of the family Flavobacteriaceae. The sequenced genome is 2 562 781 bp with one chromosome but no plasmid. It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon. On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov.

Noncontiguous finished genome sequence and description of Necropsobacter massiliensis sp. nov.

Strain FF6(T) was isolated from the cervical abscess of a 4-year-old Senegalese boy, in Dakar, Senegal. MALDI-TOF MS did not provide any identification. This strain exhibited a 95.17% 16S rRNA sequence identity with Necropsobacter rosorum. Using a polyphasic study including phenotypic and genomic analyses, strain FF6(T) was an aero-anaerobic Gram-negative cocobacillus, oxidase positive, and exhibited a genome of 2,493,927 bp (1 chromosome but no plasmid) with a G+C content of 46.2% that coded 2,309 protein-coding and 53 RNA genes. On the basis of these data, we propose the creation of Necropsobacter massiliensis sp. nov.

Update on blood culture-negative endocarditis.

Blood culture-negative endocarditis is often severe, and difficult to diagnose. The rate of non-documented infective endocarditis has decreased with the advent of molecular biology - improved performance for the diagnosis of bacterial endocarditis with blood cultures sterilized by previous antibacterial treatment - and cardiac surgery - access to the main infected focus, the endocardium, for half of the patients. Blood culture-negative endocarditis are classified in 3 main categories: (i) bacterial endocarditis with blood cultures sterilized by previous antibacterial treatment (usually due to usual endocarditis-causing bacteria, i.e. streptococci, more rarely staphylococci, or enterococci); (ii) endocarditis related to fastidious microorganisms (e.g. HACEK bacteria; defective streptococci - Gemella, Granulicatella, and Abiotrophia sp. - Propionibacterium acnes, Candida sp.): in these cases, prolonged incubation will allow identifying the causative pathogen in a few days; (iii) and the "true" blood culture-negative endocarditis, due to intra-cellular bacteria that cannot be routinely cultured in blood with currently available techniques: in France, these are most frequently Bartonella sp., Coxiella burnetti (both easily diagnosed by ad hoc serological tests), and Tropheryma whipplei (usually diagnosed by PCR on excised cardiac valve tissue). Non-infective endocarditis is rare, mostly limited to marantic endocarditis, and the rare endocarditis related to systemic diseases (lupus, Behçet).

High-quality genome sequence and description of Bacillus ndiopicus strain FF3(T) sp. nov.

Strain FF3(T) was isolated from the skin-flora of a 39-year-old healthy Senegalese man. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry did not allow any identification. This strain exhibited a 16S rRNA sequence similarity of 96.8% with Bacillus massiliensis, the phylogenetically closest species with standing nomenclature. Using a polyphasic study made of phenotypic and genomic analyses, strain FF3(T) was Gram-positive, aeroanaerobic and rod shaped and exhibited a genome of 4 068 720 bp with a G+C content of 37.03% that coded 3982 protein-coding and 67 RNA genes (including four rRNA operons). On the basis of these data, we propose the creation of Bacillus ndiopicus sp. nov.

Outbreak of adenovirus type 1 severe pneumonia in a French intensive care unit, September-October 2012.

We herein describe and analyse the first outbreak of severe pneumonia caused by human adenovirus type1 (HAdV C type 1), which included immunocompetent patients in an intensive care unit (ICU) of Marseille, France, and occurred between September and October 2012. Seven successive patients were diagnosed by HAdV specific real-time polymerase chain reaction with a positive bronchoalveolar lavage. After the collection of nasopharyngeal swabs from healthcare workers, three nurses working night shifts tested positive for HAdV C including one that had exhibited respiratory signs while working one week before the outbreak. She was the most likely source of the outbreak. Our findings suggest that HAdV-1 could be considered as a possible cause of severe pneumonia even in immunocompetent patients with a potential to cause outbreaks in ICUs. HAdV rapid identification and typing is needed to curtail the spread of this pathogen. Reinforcing hand hygiene with antiseptics with demonstrated activity against non-enveloped viruses and ensuring that HCWs with febrile respiratory symptoms avoid direct patient contact are critical measures to prevent transmission of HAdV in healthcare settings.

[Infective endocarditis due to Bartonella henselae following a rupture of a cerebral aneurysm]. / Endocardite infectieuse àBartonella henselae précédée par la rupture d'un anévrisme cérébral.

We report a case of severe aortic bicuspid valve endocarditis, revealed by global cardiac failure without fever, in a 38-year-old man who had developed cerebral mycotic aneurysms nine months earlier. PCR analysis of the excised aortic valve and serological tests (even 9 months earlier) were positive for Bartonella henselae. A combination of intravenous then oral doxycyclin at 200mg/day and intravenous gentamycin at 90mg/day was given for 6 and 2 weeks respectively. The evolution was favorable on follow-up, 12 months after completion of the therapy. Only 49 cases of B. henselae endocarditis have been reported to date, none with associated mycotic aneurysm but most often located on the bicuspid aortic valve, and usually with severe valvular damage due to late diagnosis.

Coxiella burnetii infection of aortic aneurysms or vascular grafts: report of 30 new cases and evaluation of outcome.

Q fever is a zoonotic disease caused by Coxiella burnetii. Polymorphic, the disease may present as an acute or chronic infection. Vascular infections are the second most common form of chronic Q fever, following endocarditis. Herein, we studied the outcome of 30 new cases of aortic infection caused by C. burnetii using uni- and multivariate analyses. The outcome of ten cases previously reported by our team was also updated. Of these 40 patients, 32 had a follow-up of >or=3 years. Among them, the overall mortality was of 25% (8/32). Vascular rupture was significantly and independently (multivariate P=0.03) associated with a lethal issue, whereas vascular surgery was significantly associated with recovery (uni- and multivariate P<0.01). Our findings demonstrate the critical importance of surgery in the management of C. burnetii vascular infections.